Closing and opening bot will takes a trading fee. If you often open and close a bot, you will pay several fees. Since usually negative funding fee value is small (something like -0.001%-0.01%) , you can take the loss instead of paying double fee for opening and closing the bot
Of course if you feels like the funding fee will keep negative in several weeks, it is better to turn it off and pay the trading fee rather than to take 2 weeks of negative funding fee. You can make your own decision whether to stop or to keep continue expecting the funding fee will turn into positive.