I was suffering the same annoyance until today.
Preferences > Profiles > Text > Regular Font > Change Font and play with the font Size and/or Vertical Character Spacing. Test your changes by making an adjustment, resizing iTerm, making another adjustment, and rinse/repeat until the window size lands where you want. On my MBPr, using the Monaco font, a Size of 10 and Vertical Spacing of ~1.25 did the trick.
Edit—Another possible solution:
For the Default profile, open
Window and set
Settings for New Windows > Style to either
Bottom of Screen or
Top of Screen and
Settings for New Windows > Columns to
New iTerm window title bars will be hidden and iTerm will be flush to the menubar but it's not possible to resize or move the window without first dragging out the iTerm tab (mine are bottom alined so you can't see them in the screenshot) at which point the title bar reappears, taking us back to square one.
I was able to use a pre-made Moom preset to move the window into place without the title bar present; that's how in the following screenshot I got iTerm without title bar positioned on the right: