If swallowing semen caused throat infection does that mean the semen was infected with an std or is it an intolerance to semen?

Either or: Stds can definitely cause throat infections. Semen can also be irritating to the throat and not tolerated. However throat infection may have had nothing to do with semen. Infection may already have started, or was "brewing" and would happen irrespective of semen. Or semen may have "stirred" it up a little and made you aware of the throat infection.

Difficult to know.: Semen containing infectious organisms usually has to hit the back of the throat or the tonsils in order to initiate infection because salivary enzymes often destroy most organisms, but perhaps not all. Have seen pharyngeal and tonsillar gonorrhea, syphilitic lesions on tonsils, tongue and buccal mucosa. You should be thoroughly checked for std's including HIV and protect yourself in future.