Ensuring Affiliate Payment After Opt-In

This is 100% correct. I stopped even bothering with Vendors who capture leads before the sales page, (even though it's common practice) because I will not get the sale if the vendor ends up making it themselves....

It's a definite issue with the cookies that I wish Clickbank would fix.Or offer their own email marketing services so everything could just be connected better and this wouldn't be an issue.

I thought these were both answered in the responses above.

If you want to create your own non-buyer list, by all means set up a lead capture page and send your own traffic to it, either free or paid.

If you want sales, recruit affiliates to send their traffic to your sales page. Do NOT try to recruit your affiliates traffic onto your own list (that's the equivalent of asking them to give you their leads without compensation).

As I said before, a lead capture is fine if you feel the need to build a freebie list, but that activity is separate and distinct from product sales, and you should NOT attempt to build a list off the backs of your affiliates unless they are compensated for every lead (not just buyers).

Personally, I tend to think of my affiliates' lists as my own. They generate the leads, manage the lists, and do the mailings. Think about all that entails, and then realize that I don't have to deal with it at all. Instead, I put that effort into recruiting new affiliates, creating affiliate marketing aids for those affiliates, new sales campaigns for them to promote, etc.

I do collect the emails of my customers as part of the sales process, and then use those to send back end offers, or announcements of new products I create... or to solicit customer testimonials, or more affiliates that have first hand experience with my products.

Any good affiliate management system should easily collect the buyers list for you and will identify which affiliate is responsible for referring a given sale. MD5 hashing isn't required to do this.

Basically you can't. Most, if not all, affiliate networks use a 'last in gets the sale' system. So in your example above affiliate B will get paid.

The commisson does not really 'rightfully belong to affiliate A'. They will have signed up to the T&Cs of the affiliate network who would have defined the circumstances that generate an affiliate commission.

Only an action by the buyer should update cookies. Stuffing cookies (even if you feel it better serves your affiliates) is almost certainly against t&cs and likley to get you banned from the affiliate network.

Consider this. Affiliate B will expect to get paid and if he doesn't he will be rightfully agrieved. If you manipulates the affiliate process so he doesn't get paid, do you think he will promote you again?

As I said earlier...
you should NOT be collecting leads on your sales page. Firstly, the opt-in form is a distraction - a separate call to action - for which the affiliate will not be compensated. Most affiliates will NOT send traffic to a page that contains any call to action other than a buy button.

Tony answered this correctly, above. Affiliate A has no rightful claim to the commission on this sale.
Think about this for a minute...

Assume that Affiliate A sends a prospect to your site, his/her affiliate id is cookied on the prospect's machine, but the prospect leaves your site without buying.

What if Affiliate B signs up for your affiliate program 30-60 days later and then sends his traffic to your sales page? Should Affiliate A (who promoted one time, ages ago), and done nothing since, be awarded the commission on the sale that was obviously a direct result of Affiliate B's efforts?

I think not.

Rather than set up a promotional "campaign", too many affiliates promote ONE TIME, and then go looking for something else to promote in their next mailing. While they would love to capitalize on the fact that their cookie was placed on the referral's machine... their subsequent lack of effort in promoting the original product will invariably cause them to lose sales to the more pro-active affiliates.

This is doable, using code to collect the original affiliate ID and pass that ID as a part of the opt-in form to your autoresponder service. GetResponse and Aweber both have the ability to store this as a custom field with the opt-in info, and your autoresponder messages can include that custom field as a part of the link in your emails so that Affiliate A's cookie would be stored on the prospect's machine again - but does he/she really deserve this level of effort... and are you now doing a disservice to Affiliate B by overwriting his cookie with Affiliate A's?