I have the EOS 300D, which has no mirror lock up (without resorting to hacked russian source code). My longest lens is the 100-400L. If I take a picture through the lens on my tripod at a slow shutter speed (with IS off) it always comes out blurry. I tried using a bulb so I wouldn't touch the camera, but it barely helps. I'm guessing my mirror slap is making the whole thing move.
The advice to turn the IS on is sound, that would probably solve your problems.
The mirror slap on the Digital Rebel/300D is especially barfucious, because the mirror slides back and then up to clear the back of the 18-55 lens. (FWIW, the old Miranda G's mirror worked in much the same way, but it had a nice lever actuated MLU like the Canon FT, next to the lens mount) Placing a light camera at the end of a lever arm (from the tripod socket of the lens to the center of gravity of the camera body) isn't helping matters, because the mass of the 300D is so low, it wants to oscillate with the impulse of the mirror impact. If you think about it a minute, it is probably more stable (has more inertia) when handheld, because then the body is mechanically coupled to the mass of your arm.
I think the easiest thing to do is temporarily increase the mass of the camera body by draping a bean bag over it, and/or by using the auxiliary battery pack BG-E1 (expensive). I'm constantly amazed at how much sharper photos taken with my old EOS1 are when I've got the PB-E1 on it, tripod, monopod, or handheld.
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