What gives?
First, have you looked up the value of the used car anywhere? You don't give much info on these cars. If it's a year old CPO with only a few thousand miles, and it's a Honda.....yea, you're not going to catch a significant price break.
The sticker price was $4K less but he said he'd knock $2K off the new one.
Manufacturers sometimes have rebates on cars. Have you looked up what the Honda rebates are? If not, you absolutely should.
sales rep at the Honda dealership was pushing her towards buying a brand new car
If the difference between new and used is $2k, I'd probably suggest that too.
My assumption is that there's something he's not being honest about
I think you just need to do some research, it sounds like you have done much at all...
Research the vehicles worth, There are tons of websites that can help give you a ballpark as to the used cars costs. Every used car is different, but you most certainly should be able to get a rather good estimate from searching for similar vehicles and using sites like kbb.com and edmunds.com.
Visit TrueCar, see what others are paying for the same new car you are looking at.
Once you know what each vehicle is worth, and you have a dealer with solid reviews, go there and assuming you like the car, tell them you'll buy it for the price you found to be fair.