What use is a transaction that is never relayed?

None, unless it is generated by the same person who mines it into a block. But it is not the case that non-standard transactions are never relayed. There are nodes that relay non-standard transactions and miners who include them.

How did the transaction make it into a block in the first place if it cannot be relayed? Did this transaction come directly from a client? Was it created at an origin node and put in a block somehow by that node?

Nobody said it "cannot be relayed", merely that this particular piece of software does not, by default, relay it.

What does it mean that the script is "accepted" if it's "in a block"? (I'm aware of the script evaluation process, but the sense of the word "accepted" here doesn't seem to be the same as the standard "evaluate to true" verification process.)

It means that the client cannot reject it or otherwise ignore it. If it gets into a block, it's officially done and its outputs are spendable if the transaction script rules say si.

Perhaps most importantly: What good is all this wonderful scripting capability if interesting transactions are not relayed? Won't this cripple the scripting capability for more complex transaction types?

That's a good question.