Hmm, I'm really split down the middle on this.
On the one hand, I'm a Linux user, and I certainly wouldn't mind dealing with these small inconsistencies (even if it meant that I had to edit every mod I downloaded before playing it), so I think that, soundlib problems aside, I would be happy with that the way it is.
One the other (and very much bigger) hand, this is your baby. You've hit the big-time with this (and deservedly so), and it's a labour of love for you. You're very proud of it. You don't want to see it compromised in any way whatsoever; you don't want to see people complain, which they inevitably would, if there were these kind of 'issues'.
While it's obviously not my business in the slightest, I'd advise leaving off a Linux port for a while. Who knows, maybe you could hire someone to take care of it once the cashflow is going your way, although I doubt that's an ideal solution! But at the moment at least, it does seem like too much trouble, especially as you must be going through some pretty rough testing/final stages right now.
@sakuramboo: Yes, but modding this game won't require C++. For simple mods, I'm guessing Photoshop(/MS Paint) skills and basic use of the ingame editor; for more advanced mods, all of the above plus a bit of high-level scripting.
On the subject of case sensitivity: from my