I think they should waive the fee if you can't book it online, but they're basing their "yes we will charge the fee" position on stated rules, not some notion of "consumer fault."
Why would they waive the fee? Its not the frequent flyer friendly thing to do.
SQ gets away with a lot because of their reputation. Obviously they're not telling us why they started blocking SQ online, but I think its fairly safe to say that, like LH, SQ isn't wild about showing what their (premium in particular) award availability is, to one of the largest FF bases in the world. In line with United massively jacking up their award pricing for partners, I suspect they are at least more than happy to make it harder for customers to force UA to buy SQ award inventory.