I need to access and modify the standard div property scrollTop but the securityDOM does not use this. The security Review doesn't allow jQuery to be used in a controller script, so I need another way to access the property.
The security review process for AppExchange should not be stopping you from manipulating DOM elements that you own in a controller method - that was a misunderstanding that we have supposedly corrected. That guideline was for DOM elements that were created on your behalf by Lightning's default renderer. Please loop me into the security review for your components/app submission to AppExchange (DM me at firstname.lastname@example.org) if you are still being told this incorrect information.
We will be fixing the omission of scrollTop, scrollWidth, etc soon (tracked by bug W-3189035).