This sort of thing is nothing new. Nintendo whored out Link to have him in Soul Calibur 2 on the GC. They also had Mario have cameos in all sorts of unrelated games, such as Punch Out where he was the referee. So its not like this is without precedent. Now, did having Link appear in SC 2 "cheapen" him or the Zelda franchise? No, it didn't. People don't even talk about it anymore. I think the same will be true with this DOA game in a few years.
Ironic as this may sound, I think Other M (which is an official Metroid game) has done far more damage to the franchise than this DOA thing ever could. As far as Samus being sexually exploited, that will probably happen in DOA, but that isn't something new either. Nintendo has been doing it for years. So again, having Samus parade around in spandex in DOA isn't anything new, because she does that in Smash Bros, Other M, you name it (well, actually not in the Prime games so much). But yeah...