Yes, if you root but don’t install a custom ROM you will have a stock
phone on which you can remove or install any app you like. However,
you’ll have to remove items like CityID by hand (see the bloatware
section of this guide), whereas a ROM will remove them for you.

As an FYI, the guide is written to show people how to root and do
everything without using a ROM, but I am personally using Virutousrom.
Virtuousrom is a very stable ROM and is as close to stock as you can
get. The ROM gives you an app called Virtuous Buddy that allows you to
turn on and off bloatware (like CityID) and enable/disable services like
Facebook for HTC Sense. If you want to stick with stock I’d recommend
Virtuousrom, as it makes life a whole lot easier.