I think the two of you have a very good debate going on here, and I can see where both of you have some good points.
As far as who gets the nod, I think both of you are right and both of you are wrong.
In Fenix's defense:
Going with something like an accoustic guitar track with little or no bass cutting is a very ideal, purist way of doing things. But unfortunately, it's not living in reality. At the same time, if you are forced to severely alter and contort the sound of it - or any other track for that matter - I would be worried about other issues: You need to reconsider your mic choice, or it's placement, for one. In the case of an accoustic guitar, GET IT AWAY FROM THAT SOUND HOLE. CHANGE YOUR STRINGS! Consider ditching that LDC and grab something with a smaller diaphragm. Often, these steps can give you a sound that isn't as full, but doesn't annoy the fuck out of you when soloed either.
If something needs to be messed with that drastically, I would have to wonder just how necessary it is in the mix in the first place. As nicely as you can, ask your talent how important that track really is.
In Shailat's defense:
Even though Johnboy Walton claims to be a deaf newbie, he brings up a seriously thoughtful point: Tracks don't exist in vaccums. Johnboy mentions Dream Theatre's guitar and bass as being more like "one instrument" instead of two separate ones. The bass acting as the "low end" to the guitar's mid/top end. Ideally, the bass guitar will also act in harmony with the bass drum to create one sound.
So if you solo either of these instruments, you will probably say to yourself: "Damn, this sounds really . . . incomplete in solo mode." Well duh, that's because you are only hearing half of the "real" instrument. In Dream Theatre's case, the real instrument is actually the interaction of the guitar and bass together. I suppose you'd probably come to the same conclusion if you were to listen to a guitar with the low E, A, and D strings missing. I'm sure that would sound pretty bad, too, but much improved once you add the other strings.
On that train of logic, I suppose you could solo the various tracks in a harmony vocal and think "Hmmm, something just missing here. It's like I'm only listening to one voice that isn't even the melody."

And I know a lot of people who have outstanding voices for harmony, but you'd NEVER want to hear their voice in solo mode ! !