They are basically an Internet-based bank. Like any other bank, they have rules they have to play by, and there really is very little danger of problems associated with them having your bank account number. Every person or company who recieves a check from you (or handles that check) potentially has your account number.
PayPal is an excellent way of *instantly* receiving funds from Internet sales, and allowing people to buy things on their credit card without you having to (try to) acquire your own merchant account.
As far as their web-store rules: they were probably advised to make those rules by their (PRK-based) lawyers to cover their a$$es. Considering how much gun-related merchandise is purchased and paid-for via PayPal daily, I don't really think that it's that big of a problem. They just have a policy about the web STORES that THEY host.
It's one thing to protest/boycott a company that has a clear anti-gun position, but if you were to try to boycott every company with some kind of weapon-related policy, you'd need to grow your own food and weave your own clothes, because these policies are nearly universal these days...