First, let me freely acknowledge that I am one of the biggest whiners among the true believers when it comes to the prior Hobbyist tendencies of the Property. Just tonight in fact I made a passive-aggressive comment on the Mythmakers situation.
That said though, I've rarely had a problem with the quality, or appropriateness of side treks, just their bloody frequency.
Also, while the reigning d**k of never-misses-a-day web comics over at LICD hasn't ran a single guest comic EVER, every other professional or semi-professional comic I read does run them. Now I can't say I read them all, or even all the professional ones, (Penny Arcade being one I don't, and that may apply) but that seems to be a pretty solid rule.
We all know WHY you need the breaks, and you'll never hear anyone who isn't trolling say that they'd give up some of the amazing quality on the books for a shorter down period. Still, if you want to take the 2 week down time to run a Starkweather preview of 5 pages, an Angels/SG cross-over strip a bunch of Sporkbot and Master-Futon's better pieces, or even just the rest of that Mysthmakers story, all of that is fine. Piro does it, and he's published with DC now. Scott Sava does it, and he's at 1022 with only a single unplanned down time, and he's selling his comic for movies.
The professionals do it. They just make sure that it's 6 strips max in between 32-90 solid posts of on-time awesome sauce. That's all I ask