The difference is very relevant here. Stallman believes that developing closed source software is morally wrong, much the same way that some folks believe abortion is morally wrong. The Open Source "movement" believes that opening the source leads to technically superior software. Linus open-sourced Linux because he thought it would be more useful that way, not because he thought that he was doing something morally right.
The OP here apparently came to an agreement with his partner that they not open source the good parts of the code. His question about it being "wrong" to open source the "good stuff" seems to come from a moral perspective. From a moral perspective, I think he's on fine ground. If he's worrying about making the most money, it depends on what he considers his company to be. Are they are hardware shop first and a software shop second or is it the other way around? If it's the former, open source it all. If it's the latter, he should close everything up if money is the only issue at hand.