What sometimes happens is that a crook may join an affiliate program and then use a stolen/hacked PayPal account or credit card to make a purchase through their own affiliate link, under the mistaken impression they they would instantly get paid a commission on that sale. However, we do not pay out commissions instantly nor automatically, and any calculated commission would be revoked when the legitimate account holder discovers the unauthorized payment and gets it reversed. If you see a lot of reversed payments referred by the same affiliate, you can remove that affiliate from your program, which bans them from rejoining.
This subsection of our affiliate system help page explains how merchants actually pay out commissions to their affiliates:
You can minimize bogus commissions by waiting until near the end of the month to generate your commission report (masspay.txt file) for the previous calendar month -- e.g., wait until near the end of March to generate your file for commissions earned in February. This should allow ample time for reversals to be processed for any payments in that month, revoking any commissions earned on those payments; once you generate the file, you could even hold onto it for another month before using it to pay out commissions, in case you wanted to watch for any late-breaking payment reversals and manually adjust commissions for that month accordingly before paying them out.
Regarding your suggestions, some of those we'll have to add to the wishlist for consideration as a possible new feature, others are already possible:
All account registrations in our system require the user to provide a valid email address; we send an activation code to that address which they must enter in our system to activate their account.
You don't have to make your affiliate program open for anyone to join. In your Seller Admin > Affiliate Program Settings, you can disable "List affiliate program in E-junkie Marketplace", so product listings you've posted to an E-junkie Shop (which also appear in the general E-junkie Marketplace that existing affiliates can search) would not show any affiliate program details or sign-up links. Your Affiliate Program Settings also provide affiliate sign-up link code to paste on your site; however, if you don't paste that sign-up link code anywhere, nobody could join your program unless you personally provide them with the link URL from that code, which would look like this (the X and Y parts would be unique to your own sign-up link):