Here's some things you can do:
1. Rhythm/Fuzzy Guard
If your opponent doesn't time Throw to hit on the same frames a button would connection, you can Crouch Block > Release Block > Block in time with the throw window. This will allow you to block most things like meaty hits, while netting you big damage on a reaction d2 throw punish. This is especially nice on wakeup since you can do this after delay to further mess with the opponent, but it works best in situations where the opponent wants to throw with predictable timing, such as after d1.
If they use the d1 frame advantage to go into a slower option (Perhaps a strong mid starter), but buffer throw out of d1 recovery, you'll defend against both options.
2. Always break so that if they're right, you get thrown out of the corner, or put in a more advantageous position.
Throws aren't actually a 50/50, given that most characters can lose the corner on back throw. This is a huge positional disadvantage. If they want the throw, they have to give up positioning. This will allow you to win by attrition even if your opponent is successfully mixing up his throw directions.
Depending on the character matchup, you can shut down any subsequent offense.
I feel like I should remind everyone you get a chance at the break window on reaction.
If you haven't implemented either of these in your play, you weren't completely playing MK to begin with, so why complain about throws?
