Unless there are real size issues (more kids than coaching staff can manage to keep in line), I don't think there should be cuts as long as the kids are willing to try. I've seen multiple kids transform from 28-32 min 5k XC runners as freshman to solid contributing 18-19 min runners by junior year. This would never have happened if the kids were cut and not given decent guidance. As a HS or earlier coach, leading these kids to put in the work and make huge gains should be considered your true triumph, far more than squeezing 10 more seconds out of the super-talented kid who is a star from day one.
There are fine solutions to all the issues mentioned, like only taking varsity kids off-site to run. Someone mentioned slow kids holding up a meet - is the extra 15 minutes at the end of one JV race really that big of an issue that you won't give kids a chance to be part of a team experience, or a chance to improve themselves?
This isn't a sport like basketball where the number of courts or number of players who can get into a game is a limiting factor.