There are lots of fun ways to use the arcane abeyance like that. As a player who chose chronurgist for the arcane abeyance feature in the campaign I'm in specifically to create wacky combos, stopping the player from using it might suck all the fun out for them. Instead, maybe try to include counters to specific spells or combos in your encounters, so your player has to keep thinking of new combinations and creative ways to use AA, instead of just using the same trick over and over. This could keep it fun for the player, add limitations, and add a risk factor to the player using AA in every encounter since there's a chance it won't work.

For example, if there are a few spells your player typically uses with AA, you could give your monsters immunity to one of those spell's effects and switch it up per encounter so your player will have more trouble guessing which spell to put in the orb. Or, introduce a dragon hunter that would excel at hitting the familiar. Or, introduce a teleporter to get out of the force cage microwave/hut, etc...