Using the PlaceAtMe command in Oblivion bloated the save file. Does anyone know if this is the same case for Skyrim? Is it safe to use in scripts and such?

It will bloat it too, afaik.

It will only bloat your save if you leave millions of objects lying around. Just mark them for deletion when you do not use them anymore, that's all.
Now if you need millions of objects to stay around, it's your mod's fault, not PlaceAtMe's.

Would disabling them and deleting them upon leaving a cell not bloat my save?

PlaceAtMe was not a great idea in Oblivion because there were no script functions to delete the created objects when you were done with them (well, only FullActorCopies could be deleted) until OBSE 17 added a DeleteReference function. Skyrim has a delete function by default, so as long as you remember to delete and References created with PlaceAtMe, no harm will be done.

If you delete all spawned objects anytime the player move to another cell then yes, you will be fine, no bloating.