The best thing I can think of, is something like CutePDF or some sort of print-to-PDF type program that you can install. Then at least you can go in and selectively choose not to print certain pages if it's only a footer or something like that. It's far from perfect, but it's certainly better than you've got now.
IE has had issues with printing since probably at least IE3 or IE4, meaning Microsoft clearly is in no hurry to fix this issue. So if the site you use isn't willing to help, and changing service providers isn't an option, my suggestion adds an extra step or two, but you can sell it internally by saying it will save on paper and toner/ink, which in either case, can be expensive when we're talking color. You could also use that same money saving argument to lobby for a better browser like Firefox or Chrome, which does not have issues with printing.
Let me explain. I'm an IT person at a small office. We have an Active Directory local network with a set of restrictions applied to workstations. Due to this we can't use any good web browser and have to stick with IE 9 because it seems to be the only browser compatible with the AD. But what it seems to be lacking (well, besides 20 other things) is an ability to provide good options to print web pages. Here's what we need:
1. Ability to set the scale of the page for printing. We need this to be able to print our financial reports. Unfortunately the company that provided the web site where we print from (Authorize.net) does not seem to care about how much paper we waste by printing their reports and thus we end up throwing out last pages because it prints a footer or some non-sense on it. (And having contacted support at Authorize.net I don't think they will add printer-friendly pages any time soon.)
2. It would be also nice to be able to control how a page is stretched horizontally, so that the content on the right side doesn't get cut off during printing.
3. Ability to set printing in landscape or portrait orientation and make it remember it!
4. Ability to print a web page with colors on it. We need this to be able to print the Google calendar page.
I know that IE 9 does some of this stuff, but the settings don't stick. In other words, once the browser window is closed someone needs to enter them in the print settings again, which is very cumbersome.
So my question is, is there a plug-in for IE 9 that could provide extended printing capabilities like I listed above?