How about limiting people to doing these operations a MAXIMUM of say three a day (regardless of how many characters they have)
Weekends I average 10 STFs per day, weekdays average 4, so average of 160 STFs per month. It has taken me 2-3 months to get all my ground gear and space weapons. So instead of 2-3 months to get all I wanted on one toon it would take 5-6 months. So to fully outfit all 8 of my toons it would take 40-48 months (3-4 years). I guess thats one way to keep us grinding.
Yeah right people are already complaining about the drop rate and how long it takes to get gear, if Cryptic then started restricting how many STFs someones handle could on per day, yeah that won't go over to well, starting with this user.
Restricting how many STFs a users handle can do to the only system that is keeping a major percentage of people in STO will do one thing, User signs on and does the Maximum amount of STFs and signs off.
The best thing Cryptic could do, is get rid of the STF cooldown (or reduce it) and Death Penalty Timer that would help fix the problems with griefers ruining an STF. "Ah we got a griefer exit and reform team."