I don't see how a CTP is different than an ace pot in this example. Everyone puts in a certain amount of money for a chance on certain holes to win more money back. Some people get to play those holes, some don't.
The leagues around here that have ace pots are flex starts and you can start on any hole you want. I guess if the weather is sketchy, then everyone should just run to the part of the course where there are 3 ace runs back to back to back instead of going to the harder par 4s. This would cause a big backup at the course and some people might not even get to start their round before the weather starts... I guess those that don't even get to start don't get their ace pot back?
Look, you obviously know more about your league and whatnot so im not gonna argue about it with you anymore. Do whatever you want.
I would offer these bits of advice;
Structure your league better. If there are many teams at the start, have them start on several holes. If you come late, you can get in when there is a gap on hole 1.
Whatever you decide to do w/r/t ace pot/payout/hole min etc, put it in writig and stick to it.
My suggestion, pay out aces, and remind everyone of what your SOP is w/r/t weather cutting league short and what happens with an ace.
Good luck