How can I tactfully decline my supervisor's suggestion and set boundaries?
5h commute a day for 2 weeks is not acceptable, pandemic or not. To play it tactfully, I would ask the supervisor to pay for accommodation there for these 2 weeks. This will force your supervisor to:

pay for it, so reconsider whether it is worth it.
if she pays officially for it, she must check whether that trip is authorized by the university considering the pandemic, I know mine has forbidden all travel.
I think it is reasonable to ask for accommodation but would end up being a graceful way of dodging the bullet.