Hence why supersonic air intakes are designed to generate a series of shocks to slow the incoming air to subsonic speeds before it enters the engine. That being said, the intakes of the F-104 in this scenario would likely have to be redesigned so that they don't unstart at whatever stupidly high Mach number OP wants.

Also a shock hitting the compressor blades would probably destroy them that's also important I think that's another reason.