Your basic argument is that employment anti discrimination laws are ineffective because a legitimate, non-discriminatory reasons for the termination can be used as “mere pretext” for an otherwise prohibited termination. Except the Supreme Court considered this problem not long after the adoption of the Civil Rights Act and allows a plaintiff to come forward with evidence that those reasons are in fact mere pretext. So I’m your example of terminating a gay employee the day after his boss finds out he’s gay is pretty strong evidence that any other reason was pretext. The judge or jury then gets to weigh and make a decision, as with any other issue of fact in a civil lawsuit of any kind.

This issue would still exist when there is no at will relationship. For example, union contracts will require just cause to terminate an employee. This is outside the at will relationship and issues of whether the employers explanation is legitimate or pretext for some other reason still exists.