A player having access to counterspell is need-to-know DM information just like a player having access to flight is. It can and should be planned around.

Also, if the player and DM are into it, escalate the arms race, start having enemies prepare counterspells. Lots of interesting casters have it on their lists but DMs are afraid to use it to its full potential. Players would do it to enemies all day long but when the tables are turned, nobody ever forgets what it’s like to have the enemy lich counterspell their heal.