I'd say go ahead and use the Stam morph if you want to. Things like damage and such now scale based solely on your highest-cap resource, not specifically one or the other. So if you want to use Cephaliarch's Flail with your magicka build for big bursty damage, go right ahead! It won't impact anything too important. Sure, you won't be able to spam it, but by the time you build up the Crux to cast again, you'll probably have regenerated that stamina again.