Hmmm, there may be an issue with your setup. Even in daylight in my living room the available light is not much but I don't have "many" problems. Another thing I do with my hotshoe flash (430ex II) is similar but instead of a pre-flash it projects the af assist beam (red lines that cover focal points), this is far less distracting but also requires an semi-expensive flash unit.
In full auto mode I am unsure if you can truly disable the flash (never tried). Since you are an old 35mm user I would dive back into using AV, TV, manual etc... Auto is nice at times but having a good grasp of the other settings helps when you need to use them.
60D - Sigma 30mm 1.4 - 50mm 1.8 ImkII - 18-135 IS - 70-200 2.8 mkII - 2x430ex II - 3xFlextt5+AC3 - Einstein 640 w/mc2 - Vagabond Mini