[_ah]

Sounds like this is a small shop. When you were off by yourself, your compensation stood alone in its own category. If you join the other backend devs, then your salary is compared against theirs and it "looks bad" on the internal spreadsheet. This is an internal political game and your CTO is not willing to spend his political capital on a junior developer. That may or may not be a reasonable decision on his part. Your excellent work up to this point (and future potential) isn't being weighed as much as it should be and there's probably very little you can do to change that.

I wouldn't accept a pay cut. It's too early in your career for that.

The ideal option is to tell the CTO "I can't take a pay cut. Keep me the same, and I promise I won't tell anyone." That might solve his political problem. If he won't go for that, then your options are: (1) continue in your current role (unhappy, but better paid), (2) leave for a different position. You probably will want to start planning for your eventual exit anyway, since this smells like a place with limited growth prospects.