OP_RETURN was not part of isStandard? from day one. Once it was supported by Core it became necessary to actually support it, not try to support it in one part of the software and not in others. The whole reason it was supported is because without it people will use more heinous methods to encode data on the blockchain. There's no way to stop people from doing that, so this compromise seemed best for everyone.
I think we should actually define "spam". To me a valid transaction someone willing pays for is never spam. Also PaymentRequests would be a very inefficient way to spam. It would be much easier to write a script to automatically create and submit transactions yourself. With PaymentRequests customers have to initiate the transaction and submit/pay for it one by one.
What is actually the worst case scenario that those opposed to this are concerned about? That this takes off like wild fire and all of the sudden millions of people are using PaymentRequests and creating small transactions? That seems like a win for Bitcoin. It will help spread support for the Payment protocol and IF it becomes a problem it's because so many people are using it. In which case there's a very valid use case for Bitcoin that people are obviously excited about.
I really don't like the idea of policing other people's use of the protocol. If a transaction pays its fee and has a greater than dust value, it makes no sense to object to it.