I see two possibilities for the answer of this question, one of which I have to believe is already incorporated into the middle or long term of this story (and personally I believe that there are 3-4 books worth of story in at least outline already planned, given all of the material presented but unexamined in just book 1 and summer updates, hence a whole forum full of speculation. Heh).
1. Wanda does form her own side. She has her own livery, Unaroyal is free, etc. etc. there are good reasons to see her doing this. But I'm not sure about the motivation. Wanda currently is pursuing which goals? It doesn't seem clear that any of her current ambitions would be better fueled by becoming her own overlord. Also; do casters become overlords? Is there any evidence of this occuring? Changes to Jillian (though not total) since she took rule seem to suggest the responsibilities and actions of ruling are incongruous to fully pursuing combat, or (probably) casting. Warlords have effects on city operation so long as they're there, so I would expect there being some similar bonus to actually having your overlord in the capital. That said, Stanley goes a field plenty, and has a hands-off management style when he *is* at GK. And they seem to do sort of OK. What Wanda starting her own side would do, is make the conflict into a three-way struggle. Way more narratively interesting, and just the sort of thing to throw at the Perfect Warlord, especially right after 80% of his troops abandon his side.
2. Decrypted have a glaring, terrible weakness, that is discovered and exploited before Wanda can pursue any such actions as forming her own side. Anyone who has played any fantasy game, ever, knows to use fire and healing/holy spells on undead. Decrypted seems to be a template (D&D 3.5-style) added to an existing unit type, different from uncroaked just being low level infantry/zombies with just a few of the abilities of the original (like flight, leadership). Arkenpliers are great, but so far it seems to have only provided benefits and no negatives (no upkeep, autonomous, memories/exp intact). Given, neither hammer or dish seem to have any downsides to their use. But making up an entire army of a homogeneous unit type, all with the same (potential) weakness, would make for an obvious counter-tactic to anyone who can discover the weakness. In this case, again, suddenly it's a narratively interesting situation to throw at the Perfect Warlord, by neutralizing 80% of his troops.
I would lean towards the second potential outcome. We know that Charlie is gunning for an arkentooler. And aside from a quick jump off the ice shelf at Charlescomm, the most exposed user is definitely Wanda in the field. You have to believe there is some kind of head-vampire mechanic where should the plier plyer be croaked, decrypted go back to just crypted. That would be quite a glaring weakness, the caster herself. Ansom got taken down with a ton of his own forces in the same hex after all. What would be interesting is seeing Stanley croak, and the dwagons all get turned loose. No warlords to keep them from wreaking havoc on everything in reach.
Personally, the GK assault on Jetstone has a pretty good parallel to RCCI's assault on GK. So I wonder which ender's game tactics (covered in Parson's Klog 3) could be employed back at GK now? Hidden weakness and foolsmate (attack GK, say, from FAQ) have already been considered. I'm hoping for a Jetstone superweapon or mass deception for Parson to overcome, though.