Given any uncountable set S, would I need to use transfinite induction to prove if I remove single elements recursively, I will be left with the empty set?
It seems like this can be thought of as an arbitrary intersection problem, so just a logical consequence. Could I do with something weaker than transfinite induction?
Yes and no. If you remove single elements recursively, you will eventually remove everything, but you need a wellordering to be able to do that in the first place. To remove single elements recursively, you have to do it in some order; it is a transfinite recursive operation. To show that it eventually removes everything, you would probably still have to use transfinite induction in a more or less veiled way, but you don't need any more “choice” to do that.
On the other hand, if you just remove every single element without caring about the order, you don't need anything like that. $\bigcap_{s\in S} S\setminus \{s\}=\emptyset$, period.