It looks like the Mega2560 has to see a minimum of 0.7V * VCC for a logic level high which leads me to believe it would have to be a minimum of 3.5V which would not work.
Strictly speaking true. However in practice you will find it most of the times it does work but it is not guaranteed.
I know the Mega 2560 has 10k pull-up resistors, but I do not know if the I2C lines will operate correctly if they are disabled (or whether or not I can even disable them).
They are hardware resistors so the only way to disable them is to remove them. Then you must disable the internal pull up resistors by using a libiary that does not enable them by default, or by turning them off with a pin mode INPUT call for both pins just after calling the wire begin.
If they were not disabled then I suppose I could put a 30k resistor in series with SCA and SDL lines to get a 40k pull-up, and then if I have the 10k pull-ups from the 3 sensors in parallel, then I would actually have about 1, 3.3k resistor.
No don't even go there, it will not work.