Plasma creation and condensation
To begin with, dissociating molecules to a plasma at the atomic level will not only create ions but also neutral atoms. These will indeed reassociate on cooling, and the question is how to predict what the products will be. In the extreme case of a simple system such as pure hydrogen gas (dissociating, then recombining to H2) or, say chlorine plus bromine dissociating/recombining to give BrCl, it should be easy to predict the products formed and perhaps more about the behavior of the system as a function of temperature. 

If you have a more complex system, including (for the sake of argument) atoms such as carbon that can form complex ring and chain structures, predicting the outcome will be impossible - since (1) the different ways to combine atoms may lead to a huge number of possible intermediates, many of whose energies/reactivity are not known; (2) even if you could predict these intermediate structures, the number of further possible reactions between them becomes astronomical, and (3) kinetic barriers (activation energies) for  reactions are generally harder to predict that ground state energies. As is often the case when theory comes up short, you may have to go into the laboratory and do some experiments. Possible approach: aim the plasma (along with a stream of inert gas such as argon) at a supercooled probe in a vacuum and spectrally characterize the species in the resulting matrix. I imagine that you could end up with some pretty amazing chemical species that way.

I would urge those among my colleagues who are familiar with the current state of theoretical chemistry to add to this discussion. I love a question that makes you go back to basics and rethink everything from the ground up.