Well, another solution to this problem, is to make the equip/upgrades PBAoE instead of the psuedo-Targeted AOE that they are now. This will prevent the need to have to target the pets, which isn't possible during the 'spawning' time, and allow you to quickly upgrade them all even if they are spawning.
Granted, I'm not sure how it will affect the animation, unless there is a 'animate out of combat only' option, though I do notice that currently only the pet I am targeting gets hit with the 'animation' issue, even if the other pets are in range of the equip/upgrade powers.
I would LOVE either a temp invuln or huge def/res boost when the pets are first summoned, but I can see that being exploited a bit...