I'm with you on the second option, think it works better without breaking the flow of the game and makes the player have to think and plan more before each wave.
I second that option. Pausing the game while building will break the fast and intense action of the game. And making the buildings stronger doesn't solve the frustration of the enemies beating you up. The second option is, by discard, the best solution. Keeps the flow of the game and solves the issue.
But make a "pause" button. Maybe someone needs to do something really urgent and can't do that while playing the game. Example: goes to bathroom. Who knows...