Originally Posted by R_Hythlodeus
By not including Pym one would actually destroy two characters: Pym, whose guilt over creating Ultron is one of his trademark characteristics, and Ultron, whose Oedipus complex is the cataclyst for his desires to take over the world.
Whedon is smart enough to know that.
However, A:EMH handled the situation quite well with Stark having a hand in Ultrons creation too. As long as it is clear, that it was actually Pyms fault, and that Pym is the main creator, there is nothing wrong with Tony working along on that project.
If I remember correctly, in A:EMH Ultron (that is the Ultron AI) was still created primarily by Pym. Stark just provided the tech and built the actual body and weaponry. The core of the character was still Pym's baby.