Sorry about the trials and tribultions. Let me jump right to your two questions:
1. I don't agree with your doc on this. His logic is only good if there is no alternative for you that will restore fertility and that is not the case unless I am missing something here. I guess if you were diagnosed with primary hypogonadism then things like Clomid become more debatable, but you didn't mention that, so I doubt that is your situation, right? So, anyway, assuming you are secondary, then you do have alternatives to HRT and you can read several of the recent threads on Clomid for some examples of that. I would go to your doctor and say, "Why can't I consider Clomid?" (I can't tell you what to do, of course, but I can tell you to have a talk about all of this so you can get truly informed. And, of course, if you feel your doc is unknowledgeable, get a second opionion.)
2. Reasonable HRT does not kill production as far as I know. There is, though, a painful transition period where the person's HRT ramps up to its old levels and, of course, the old levels weren't good to begin with, so you know what that means. However, if you were to go on Clomid, this will help.
If you can afford it, I'd go to a fertility specialist. This can be a very emotional topic for many couples, esp. women, so I'd get an expert involved.