This is extremely, extremely unfortunate. I cannot believe any developer would make such a drastic mistake as to make a Steamworks game support a Punkbuster level which would read the Steam Overlay as a threat - that's just insane.
I really wish people would better understand the nature of Punkbuster vs VAC. Really the key differences are this: Punkbuster makes loud, public examples out of players - often ones that did absoultely nothing wrong. Because people see "player kicked" messages, they think they're being protected from cheaters, when in reality, this is pretty far from the truth - most PunkBuster supported games are swarming with them on a very extreme level. Where as VAC doesn't go that route, it hides in the background, watching your behavior patterns and then dishes out a VAC ban. In many VAC games you rarely see a cheater, and when you do, they almost always have VAC bans on their account and almost always end up perma-banned if you check their account later. It just doesn't do noisy mid-game kicks.
That's on top of the fact VAC isn't nearly as invasive, doesn't have extremely terrible exploits including ones that actually use the memory scanning against the users by exploiting it and doesn't even think of recommending things like running pbsetup every single time you want to run a game.
In short, if both of these systems were real police agencies, PunkBuster would be the one stringing up people along the road all of the time to re-assure the populace they are being protected, even if those people didn't actually do anything wrong. Where as VAC operates more similar to modern police, gathering evidence before issuing a pretty firm judgement. VAC bans are also much, much harder to circumvent as they impact your Steam account, where you likely have a lot of games.
What many of you may not know is why PunkBuster is even still used, and how it's company is still in business. I've worked with several game developers and I can tell you every single one of them have zero respect for it. The word "placebo" is used very often, and that's exactly what it is: One that does more harm than good, too, since it does the aforementioned security vulnerabilities and kicking of legit players on a semi-regular basis. In short, the company uses a simple marketing tactic of making players believe it's doing well from the kicks, which they then use to sell to Publisher Producers.
Publisher Producers are the people on the publishing side of games, that honestly often have almost no technical knowledge of games. There are of course exceptions but I have, honest to God, known producers of games that didn't know how to open the console disc trays before. These people are sold on PunkBuster helping to sell the game for "cheap and easy," and they often jump on it out of sheer ignorance as to it's actual capabilities. This is then forced on development houses as part of their contract, regardless if the developer actually wants to implement it or not. In some cases, smaller developers will use PunkBuster for similar reasons of ignorance, except purely so the user base can "sleep easy" thinking cheaters are actually being stopped when, in fact, they're really not.
The mere fact people are impressed with ban lists is the entire problem. I'm sure the local police force could arrest countless people a day on every suspicion that even remotely entered their heads, too, but ultimately this means they will be simply getting a large number of "criminals" out of people who were doing nothing, while wasting every drop of time and energy on it, letting the vast majority of criminals who aren't being totally obvious do whatever they want. It's just a broken system.
The long and short of it? VAC is far superior in every single way to PB and they positively do not need to be combined - and shouldn't be, really. It's my hope that more games will be supporting Steamworks and ditching PunkBuster in the future, and I know people who have outright canceled their RO2 orders because they don't want to deal with it's insane number of headaches only to have a game end up littered with cheating anyway.
PS: My personal experience with PunkBuster has been playing exactly two games with it in the past 3 years, in which I've probably been kicked or banned dozens of times for doing absoultely nothing cheat oriented. Being thrown off servers for the act of throwing a cheat-free grenade while at least 3 people on the server are spinning in circles aimbot'ing head shots is the best summary one could ever give this hopelessly outdated product that should have a bad memory from the the early 2000s.