There aren't any BlackBerry devices that BES doesn't support. The primary purpose of Blackberrys is BES and RIM, all the "cute" stuff like BIS, Facebook, Twitter apps for the average retail user all came out the orginal design of BES.
Now that's not to say that YOUR IT Department may have made some type of choice to NOT support the Storm (or the Storm 2) but I would guess that's their choice for what ever reason.
I'm a BES admin for my company and I take pride in that there isn't a BlackBerry device that my server won't support as that's it's strength to handle any BB, from any wireless carrier.
Now the catch might be that that they won't pay for the addtional BES data service for the device or that they only support company owned devices. I'm with a smaller organization and we support any user that has a BlackBerry BUT if it's a personal device, that person is responsible for the license CAL and the addtional data service on the device.
It's may well come down to your company does not support personal owned devices since when you activate your BlackBerry to BES, you give up total control of the device to your IT department which they can limit what you can load on it, what things work on the BlackBerry down to the point they can turn the camera off, use the GPS to track you and monitor your SMS text messages so the question really is if your Storm 2 is your own personal device, do you want the IT department to have that type of control over it?
Personally, I don't control my BES users nor limit what they can do with it but I can if I want to....
Regardless of your company's email plateform, you should be able to sync email, contacts and calendar from Notes to your device, in the worst case it might not be wireless sync if you use your Desktop manager to do a USB sync without BES activation as my company uses Novell GroupWise so don't think that you have a obscure email system!
GroupWise is technically the red hair step-child for RIM!