I am currently starting a Bosmer female who is going to be a strict Follower of the Green Pact and will end up romancing Vilja, or at least doing her quest. I know that Vilja has a part of her quest where you have to get Taproot. I am just trying to wrap my head around an RP reason for this. I just can't find a good reason for a Bosmer to break the Green Pact and grab the root/harm the Spriggans.

Advice?

Well good news! The Green Pact only applies to plants in Valenwood, plants from outside of Valenwood is 100% alright.

Pretty much this, and even then several Bosmer in Valenwood are except from the Greenpact.