One of the things that this problem illustrates is how competitive Pro Cycling is. These motors can only be used for a few minutes in races lasting hours, yet that can be a deciding advantage nevertheless. Of course there is a psychological edge for the user of knowing that they have a secret weapon available.
The problem is a relative new one as it takes the same advanced battery tech that we have with cell phones and other light-weight technology to be so unobtrusive. As such, it will only get worse because this is a technology that is still improving. Next speculation is for motors that do not need to intermesh with the drivetrain but instead use magnetic fields to spin the wheels directly. Sounds fantastical to me but perhaps it can be done.
I wonder if you could use compressed air?
If the motor only needs to run for a few minutes then that could be used to give a boost.
You could also use the entire frame as to contain the air.