I kind of think that you could keep Pym around as the "Q" of the MCU. The kind of cynical and flawed, but ultimately good scientist/tech guy. Heck, you could have him mentor any potential younger heroes like he did in the Avengers Academy book. Given how much Pym/Ant Man/Wasp fans are ALREADY complaining about the changes that this movie is making, killing off Pym would really set them off (especially if it turns out that Janet IS in fact already dead at the start of the movie).
Pym as MCU Q would be awesome