That's really unfortunate. I wouldn't be thrilled about that either, but if the suite is not usable, then I don't know what else they can do.
Not redeeming the suite upgrade but still giving you the Jr. Suite is a nice gesture. It's not really their concern that you have no other plans to use the certificate. I agree the gold lounge access is great, especially with a family of four.
I can't remember if the Copley Plaza has connecting rooms or not. If they don't offer that, rather than the Jr. Suite, I would ask for a Signature Queen/Queen room instead. The Signature rooms are only marginally smaller than the Jr. Suites (390 vs. 415 feet), yet they have very nice views of Copley Square, and it sounds like that's important to you. I've stayed in the Signature King rooms at Copley before, and they are very nice.