"Mueller points out that two of the patents that IBM listed in its [threatening] letter to Hercules are included in the list of 500 patents that IBM promised to not assert against open source software in 2005."
Can't be seen as good.
They probably couldn't actually prevail on those two patents anyway, if it went to trial: a public open letter promising not to sue if someone uses the patents could be interpreted as an implicit patent license, or at least trigger estoppel.
The loophole is a contractual issue between IBM, its customers, and perhaps TurboHercules (in that the latter is encouraging the customers to violate the contract).
I don't see it having anything to do with open-source patent assertions and again I can't see how IBM's promise would be worth anything if the latter had its own loophole of a "If we sue you for other reason the 500 patents become fair game."