I base this conclusion largely on context -- so many of these references happen in connection to other more obvious covenant symbols. It is true that in other cases, the context is more ambiguous, but I'm having a hard time finding a mention of "good works" or "works of righteousness" that clearly refers to "doing nice things."
Below I'll list the nine references to "good works" in the Book of Mormon that don't occur in Alma 5. The two examples from Alma 5 will be discussed after that (in part 2), along with the references to "works of righteousness" also in that chapter. Along the way, I'll point out related covenant symbols associated with these references.
"Good works"
Mosiah 5
Therefore, I would that ye should be steadfast and immovable, always abounding in good works, that Christ, the Lord God Omnipotent, may seal you his, that you may be brought to heaven, that ye may have everlasting salvation and eternal life, through the wisdom, and power, and justice, and mercy of him who created all things, in heaven and in earth, who is God above all. Amen. (Mosiah 5:15)
This entire chapter centers on covenants. In verse 5, the people declare:
...we are willing to enter into a covenant with our God to do his will, and to be obedient to his commandments in all things that he shall command us, all the remainder of our days...The context here is important. A few verses prior to verse 15, King Benjamin says:
I would that ye should take upon you the name of Christ, all you that have entered into the covenant with God that ye should be obedient unto the end of your lives.
He then offers a chiastic form emphasizing the need to "know the name by he is called" with an emphasis on belonging to the Lord and not someone else, since
[a man] will not even suffer that [an ass that belongs to his neighbor] shall feed among his flocks, but will drive him away, and cast him out. I say unto you, that even so shall it be among you if ye know not the name by which ye are called."Therefore," he continues, "I would that ye should be steadfast and immovable, always abounding in good works, that Christ, the Lord God Omnipotent, may seal you his..."
In other words, King Benjamin desires his people to always abound in good works so that they may know the name by which they are called.
Alma 7
"Good works" shows up twice in this chapter, once in verse 24 and again in verse 27, but the preceding context is important, as was the case in Mosiah 5.In this chapter we find Alma-2 speaking to the righteous people in Gideon. He praises their righteousness and invites them to "walk after the holy order of God":
...do you believe these things? ...yea, I know that ye believe them...because your faith is strong concerning...the things which I have spoken, great is my joy.
I perceive that ye are in the paths of righteousness...I perceive that ye are making his paths straight.
And he doth not dwell in unholy temples; neither can filthiness or anything which is unclean be received into the kingdom of God...
I have said these things unto you that I might awaken you to a sense of your duty to God, that ye may walk blameless before him, that ye may walk after the holy order of God, after which ye have been received. (Alma 7:17-22)
After this, we get a list of attributes Alma desires for them:
Interestingly, he does not command them to "abound in good works." Instead, he tells them to "see that [they] have faith, hope, and charity, and then [they] will always abound in good works." The good works part is a secondary effect of their faith, hope and charity. We'll come back to this concept later.
After this, several very unmistakable covenant symbols are invoked, including a second mention of "good works":
25 And may the Lord bless you, and keep (see Numbers 6:24) your garments spotless, that ye may at last be brought to sit down with Abraham, Isaac, and Jacob, and the holy prophets who have been ever since the world began, having your garments spotless even as their garments are spotless, in the kingdom of heaven to go no more out (see Revelation 3:12). ...
27 And now, may the peace of God rest upon you, and upon your houses and lands, and upon your flocks and herds, and all that you possess, your women and your children, according to your faith and good works, from this time forth and forever. (Alma 7)
It is also noteworthy that the very next verse mentions "establish[ing] the order of the church":
1 And now it came to pass that Alma returned from the land of Gideon, after having taught the people of Gideon many things which cannot be written, having established the order of the church...
Alma 13
This example shows up in the context of the holy order with clear covenant connections:
3 And this is the manner after which they were ordained—being called and prepared from the foundation of the world according to the foreknowledge of God, on account of their exceeding faith and good works; in the first place being left to choose good or evil; therefore they having chosen good, and exercising exceedingly great faith, are called with a holy calling, yea, with that holy calling which was prepared with, and according to, a preparatory redemption for such.
Alma 26
22 Yea, he that repenteth and exerciseth faith, and bringeth forth good works, and prayeth continually without ceasing—unto such it is given to know the mysteries of God; yea, unto such it shall be given to reveal things which never have been revealed; yea, and it shall be given unto such to bring thousands of souls to repentance, even as it has been given unto us to bring these our brethren to repentance.
Alma 37
33 Preach unto them repentance, and faith on the Lord Jesus Christ; teach them to humble themselves and to be meek and lowly in heart; teach them to withstand every temptation of the devil, with their faith on the Lord Jesus Christ.
34 Teach them to never be weary of good works, but to be meek and lowly in heart; for such shall find rest to their souls.
Helaman 12
23 Therefore, blessed are they who will repent and hearken unto the voice of the Lord their God; for these are they that shall be saved.
24 And may God grant, in his great fulness, that men might be brought unto repentance and good works, that they might be restored unto grace for grace, according to their works.
25 And I would that all men might be saved. But we read that in the great and last day there are some who shall be cast out, yea, who shall be cast off from the presence of the Lord;
3 Nephi 12
16 Therefore let your light so shine before this people, that they may see your good works and glorify your Father who is in heaven.
Ether 12
3 For he did cry from the morning, even until the going down of the sun, exhorting the people to believe in God unto repentance lest they should be destroyed, saying unto them that by faith all things are fulfilled—
4 Wherefore, whoso believeth in God might with surety hope for a better world, yea, even a place at the right hand of God, which hope cometh of faith, maketh an anchor to the souls of men, which would make them sure and steadfast, always abounding in good works, being led to glorify God.
There you have it, aside from Alma 5, which will be discussed in part 2, these are all of the references to "good works" in the Book of Mormon. As you can see, a connection to covenants is easy to establish for most of these references.