Java is completely unsupported on Surface RT. I don't expect that to change due to the general hostile attitude of Oracle in working with Microsoft (and Apple, for that matter).
Flash is present but controlled by Microsoft through whitelists. I'm not sure if there's a way to submit a site for whitelisting or not, but it would be nice if there was so we could request additions like this one. I appreciate their desire to protect us, but we need an option to function too, right? :)
Surface Pro (coming in January/February) will run Windows 8 Pro and be much more suited to advanced usage. In the mean time, you could see if your company can give you Remote Desktop (better yet, RemoteApp) access to a desktop version of IE/Chrome/Firefox to use for that purpose. I'm an IT guy where I work, and I plan to set that up for myself as well.