The only exception I can think of is Zappa/Mothers live albums. Frank makes it completely obvious what he's done; he's taken live tracks and added studio stuff because in the end, what he's created musically is what counts. I've been listening to Frank's stuff since high school, so I guess this is another "other" category, since I accept this in the name of the art he's creating. But somehow I have trouble applying this same mentality to other bands. Maybe because they present it as a live album, and then it's just too obvious that it's not all live. So the honesty is indeed important.
Crimson does - or did - the same thing; most of the "Starless and Bible Black" is taken from a show in... Amsterdam (at the Concertgebouw; I think that's in Amsterdam), the crowd noise removed, and the tracks edited and overdubbed over as if they were studio backing tracks. Fripp has been very forthcoming about that fact, and in fact, has made it a crucial part of the mythology of the band (as primary a vehicle for improvisation).
Yeah, King Crimson goes the other way with it. I forgot about that. They take live recordings, remove the audience, and release them as studio tracks. Of course, they don't come right out and say "this is a studio recording" so I suppose that technically there's no deception involved, and I don't think I'd complain anyway. It's just the album. Fripp said that with the 70's band especially, there was an energy when they played live that was impossible to recreate in the studio, so he just took live recordings and worked with them. That's cool.
To me, I guess it's because studio recordings and live recordings are different creations. In the studio, you can do as many takes as you want, overdub and layer as much as you want, edit, fix, tweak, until it's perfect. Live recordings (to me) are about what the band can do in real time, single take. If you were there that night, this is what you saw and heard.
But if you're up front about what you've done (as with Zappa and Crimson), then the line becomes blurred. At some point, the track transcends definition as either studio or live, and becomes simply the finished work. You appreciate it for what it is, or not.