I think interaction prompt should take priority over reloading.
I just had an instance, where I emptied both guns into the predator after it had activated the self destruct. Instead of promting the defuse, the PC started reloading the shotgun (one shell at a time) and after I switched to main, it changed the clip before I could start defusing. Needles to say, I did not have enough time.
Edit: This is an even bigger problem on PS4, where the interact and reload button are the one and same.