They want to replace a motor for a single bad head?? How are they justifying that? What's your mileage? Absolutely just do the head regardless. I've always just rebuilt mine so can't say whether brand new heads are available with valves pre-installed or not. If they are it will surely cost you but should be less likely to have valve issues. Personally I'd get a set off rebuilt off ebay, but I've had 2 different local shops mangle my valve/seat cuts, coming out with worse leak downs than they went in with, so if you value your compression you must do a leak down after installation. Save the old head gasket and bolts for this so you don't ruin a new one only to find out the valves leak, like I have in the past. You can also spot bad leaks doing this before even putting it on the engine. Fluid is naptha

Pressure testing a cylinder head - YouTube

Some shops say they pressure test their assemblies after installing valves, I'd message before buying something like "hey I always leakdown test after installation to ensure valves are seating correctly, just wanted to confirm that you do bench test your heads so I can be confident not to get any leaks from my results, thanks" if they don't respond then they're probably bluffing to make more sales. Would still test either way.

Ishino Stone is your OEM gasket, 209Yota1 sells kits at a good price. If you've got some miles on the heads I'd probably do both sides for the couple hundred extra it'd cost but reasonable people may disagree.

ETA you should of course also check valve clearances while you're in there