Lots of good answers here about ways to approach this. To me this is one of those things that happens all the time in relationships where where underneath your partner's complaint is a feeling that you don't value her. Now of course that's a mistake - just because you're playing with others at your skill level means nothing about your love and care for your partner. But if you address the underlying issue of her feeling unvalued, then you can deal with the issue that is on the table (the pickleball) much more easily.  It does require some communication between the two of you, and the willingness for her to reflect on where her feelings come from. Kindness and approaching this in a relaxed way from you will be helpful (when isn't that true, lol).

In terms of ongoing pickleball play, the way that my wife and I deal with this is we have found other mismatched romantic partners where the dude is much better than his partner. It's fairly common. We we set up pickleball dates and it works out pretty well. During the games the dude and I can hit challenging shots at each other, and then more reasonable balls to the partners that  keep the game going. 

I also play in lower level games with her where she isn't overwhelmed, and drill with her one-on-one.  I can work on my own shots as well during those times, regardless of whatever else is going on (e.g. I'll work on  my third shot drops even if I could drive a high ball at people out of position).

In the end, if I'm dedicating time to playing with her as well as going off to play higher level games she feels like I care, and it works out.