I think that a canon slash relationship could be done with a degree of success but only if implemented correctly.
First of all, the CSI franchise has never been overly focused on characters' personal lives to begin with, and most relationships that are "canon" are merely mentioned on the side. A crime must be solved in ~42 minutes every week, so really, they don't have an infinite amount of time to explore relationships, slash or otherwise, which is precisely the reason why I think it could work.
I think that many people who believe homosexuality is "wrong" is turned off by the physical aspects of such a relationship; that is, they are unable to accept unconventional sex, or have been taught that boys kiss girls and girls kiss boys and any deviation of that is "sick." So I think that if the show were ever to try slash on-screen, they could, as many have mentioned, start subtle to test the waters (which makes sense, since save for a few mishaps we shall not speak of, they haven't really shown explicit scenes between main characters who are in heterosexual relationships either).
In this way, I don't think they will turn off enough viewers to drop their ratings, since many people are likely to tune in to see what the fuss is about, and I'd imagine a percentage of them would then become regular viewers. And quite frankly, the viewers who stop watching due to split-second hand-touching or a mention of a date need a lesson in acceptance anyway.
This has already been said, but it really is important not to fall into the stereotypes. That's probably the biggest obstacle the writers and actors would have to overcome: making a slash relationship as believable as a het one. If the characters' personalities change because of this "outing," or if the rest of the team begin treating them differently, the whole thing would disappoint even, I imagine, the people who have shipped the pair since the beginning. But if they can show that these are the same people working in the same environment, then I'd call that a success. I mean, I don't ship them, but wouldn't it be quite something if Mac overheard Danny saying something mildly suggestive to Flack, then simply gave them an amused look and kept on walking?
In my opinion, there's a fairly fine line between deep friendships and actual romantic relationships anyway, as far as emotional investments are concerned. I think that many same-sex characters on the shows are already straddling that line. It wouldn't be a huge leap to suggest that they were involved romantically.
Another reason why I think they should explore this is to see the rest of the team's knee-jerk reactions. I think it would be effective to have one of the main characters a little reluctant (emphasis on the 'little' since they are professionals who have sworn oaths after all) to accept the relationship at first, in order to represent the population of people who share the same view. Not to make it into an incredibly cliché moral or anything, but it'd be nice to show that the reluctant character eventually comes to an understanding that nothing's changed, that they are still the same friendly, funny and caring people they were before.
So, I wrote a whole lot just to say, if they treated slash the same way they treat het on-screen, it would work as well as het, which, conversely, has thus far been hit or miss. Bottom line, it'd be a challenge for everyone involved, but could canon slash work? Yes, I think it could.