JSA offers three ways of having your signed baseball card authenticated:
1. LOA with a scan of the image
2. Encapsulation via BVG
3. Sticker on the back
Some people want their items tagged and don't mind the ancillary damage. This is a service for them. JSA doesn't decide -- the customer does. JSA is neutral as to the impact on the value/appearance of the item being tagged. JSA is also not alone among autograph authenticators in offering such a service. This is a pretty common means of authenticating baseball items.
I don't think JSA has anything to explain here. But I will concur that I hate it and that I peeled the sticker off my E91 autographed McBride card because I preferred the oval of paper loss to the unsightly sticker.