Absolutely zero to worry about with this mod. I bought an 02 330 steptronic car in October 2016. Put a manual fan from a junkyard car in it and removed the aux fan. The car runs a few degrees cooler and so does the trans (my scanner gives me real time data for trans and engine temp). Keep in mind, in central Alabama where I live we see HOT and HUMID weather from April till November. I also spend a lot of time idling while making calls, even in the heat of summer a I never got above 204 F.
Think of it this way, in 2004 the BMW X3 auto came with an electric fan from the factory. Same m54 engine we have, no mechanical fan. Same story on my friends 2004 530i, it's an E60, but has the m54 engine and an electric fan and auto trans. Shoot, my 5.7 Hemi Grand Cherokee has an electric fan, it's just fine to run your e46 this way. Enjoy!