The MP count won't make too much of a difference. If you're buying the Canon for MP count, you're buying it for the wrong reason.
If you're buying the XT thinking that their kit lens is better than Pentax kit lens, then you're buying it for the wrong reason.
You've mentioned that you already have some Canon lens. Then it's the right reason for you to buy RebelXT. (make sure that your current Canon lens collections are EF mount). IF you want faster startup time, Canon is the answer; you want cleaner ISO 1600, Canon is the answer. Also, if you want to go crazy one day and buy crazy lenses such as my $1,100 18-55mm f/2.8 IS, or $1,700 70-200mm f/2.8L IS or my dream lens $7,000 400mm f/2.8L IS, these types of lenses are not (yet?, no longer?) available for Pentax.
Pentax ist*DL, is a VERY DECENT camera. If you ask me between S3 IS vs ist*DL, I'll take the ist*DL anytime. Definitely no more point-and-shoot or bridge camera for me (camera looking like dSLR minus all the perks).
Honestly, there is always something better for a bit more money out there. However, you mention about the $1,000 max budget. So for that budget I'll go with RebelXT (body only, about $700 after the current Canon rebate) and for the time being Sigma 18-125 (about $230).