You're right, finding that initial sweet spot in the first 12 hours or so takes a little doing, changing your target by a degree or two and watching how the wort reacts. Once fermentation starts you have to drop your target temp to compensate for the added heat. Can't drop it too far or the yeast will get sleepy but it has to go down far enough to avoid a big gain in temp. As the fermentation slows down you have to raise your target back up. All that while compensating for ambient temp changes around the freezer. It's not a lot of huge temp changes, just a lot of small ones. I have a web app connected to my controller so I can watch it while at work and what not. Once you reach about 5 days in and fermentation is done or drastically slowed, you can pretty much set it and forget it.
If you can get things going using the wort to control the freezer, you don't really have to worry about all that. The controller and freezer will cycle as much as they need to to keep the wort in the ballpark of your target. The key is preventing the freezer from going through the huge 20-30 degree temp swings the op was talking about.
Without the limiting algorithm that I'm using I'd probably suggest sticking the probe in a small container of water, like a mason jar maybe. Whatever you do, your target temp should always be a reference. Keep the thermowell in the wort and do what you need with the target temp to keep the wort temp where you need it. I've heard way too many people talk about their fermentation happening at specific temps based on ambient temp alone. Have to watch the wort.