Email is probably the most secure and actually not that bad of an option. You have access to the docs and can delete them, providing a bit of security, and download again later if needed.
This is less than ideal for many reasons- I end up with many versions of the same document, split between the ipad and the computer. I would like to just end the document to the ipad to work on it from home, bring it back and send it back to the computer. But, I'm not sure if that is even possible even if it were not for the government restrictions?
Also some of the files are very large and need to be emailed in separate emails, clogs up my email and takes up space on the mail server until I get around to deleting all the attachments. We are not supposed to delete emails permanently.
Depending on the IT org you may or may not be able to install iTunes as was recommended.
I have yet to receive an answer on if I can do this or not yet.
Another option, if you want to avoid using a PC, is a wireless usb stick, such as Sandisks. You transfer the files to it, assuming your security allow you to use non-approved usb devices, the wirelessly to the iPad.
If they provide secure gov't issue usb drives, such as Ironkey, you could use that so you maintain document security up to the point where you put them on an iPad.
I am not sure if this is allowed, I am going to look into it as it seems promising. I know we can use encrypted USBs to transfer documents, but a normal USB obviously doesn't help with the ipad issue.
Here is something else to consider:
Once the doc are on your iPad they are essentially insecure. Depending what is in the docs you could very well cause a security breach.
I've worked with an agency that let us use iPads/iPhones but we had to enable remote wipe via Outlook's web interface.
This is enabled
My advice - check with your IT security person to be sure you aren't committing a violation. The convince of an iPad isn't worth the hassle.