Easy option is don't be too greedy and take your time,
these hacks already speed the game up by like 10000000000x so don't abuse it too badly
I use the 600gems hack every 5-10mins and haven't been locked out since
I only use the auto-submit gold just enough so I can buy the habitats I need
The food one is the only hack that I tend to abuse and usually get locked out for 30 minutes -_- but thats because I have 3 running at once