Being "tough" like this increases your value to YC, but it doesn't always increase the long-term value of your company.
I'm sorry if it sounds like I'm saying you're doing something wrong. You're not. It's just how it works. It was the "burn the bridges" line that nudged me to write this comment.
But that would increase their own value as well. YC and WePay are in this together, there's never really a situation where something is good/bad for one and not for the other.
I understand that things are blurrier with YC than they are with VC firms in general. I know about and admire Wufoo. I know Graham has repeatedly stated how happy he is with the Wufoo outcome. I can see plain as day the network effect YC has created with the large number of operating businesses it has started and with its (even larger) alumni network. I am not picking on YC with this comment.
I think you may be right. The guy that's best to start the business is not necessarily the best person to run it a few years later. I'll let you know in a few years ;)