We have tow boats on Saganaga Lake that is in the Boundary Waters Canoe Area. We can use up to a 25 horsepower motor as can anyone who has a day use motor permit. We instruct our tow boat drivers to slow down to be courteous to people paddling even though slowing down causes a larger wake, it's perception. We also instruct our drivers to make sure none of the canoes have troubles(like getting swamped).
There are areas on Saganaga where there are reefs and tow boats must avoid these while canoeists can pretty much paddle anywhere. Sometimes canoeists will paddle 4 canoes abreast and the towboat driver has to get close to them in order to not wreck the motor.
We find most motor boat users on Saganaga, what few there are, are quite courteous to paddlers.
Before the area was made into the BWCA motors were allowed everywhere. There were cabins on the Minnesota side of Sag and there are still cabins on the Canadian side of Sag. While almost all lakes are now canoe only, negotiations were made for motors to have access to the area as well.
Almost all entry points are canoe only so in order to avoid future problems I would suggest entering at one of those entry points. There are plenty of lakes for everyone to enjoy. I hope your next trip into the BWCA is even better.