A few things.
1.) I do think it's important to raise concerns at this point in the project, especially with details yet to be unreleased. Unless concerns are raised Microsoft will do as it sees fit. It cannot react to concerns that aren't voiced.
2.) I had some of the same concerns (and still do). The "just don't use Metro" for those types of apps isn't an acceptable answer if we want to embrace a Windows 8 that spans both the desktop and tablets (because some of our users maybe tablet only). I understand this concern, I had the same one and the "just suck it up and use the marketplace" mentality simply doesn't cut it. Good news though! I read this the other day (and will provide a link)... Microsoft with the Enterprise edition joined to a domain will be providing a method to side-load Metro applications (key phrase, enterprise edition joined to a domain). This will help with a lot of concerns on how Metro can be used for private, internal applications.
Scroll down to "New Windows 8 App Deployment" in the below link: