Harmony remotes will work well. Keep in mind that the roku remotes are wifi based so you don't have to point it at the box, but using an IR remote you'll have to have line-of-sight and keep the remote pointed at the box. It'll still make everything else easier, you just might go back to using the Roku remote.
If you're already controlling everything else, and you don't play games on the Roku (games will be infinitely better on the Roku remote I reckon), I think adapting to the IR control isn't bad at all.
The only issue I've noticed at least, inputting user names and passwords is excruciating with IR remote. The Roku remote handles this much better, there is zero delay unlike with IR, yet... I hate remote-based input for my asinine-level passwords (Lastpass saves the day, except when dealing with the TV

).
However, it's super easy now: use the smartphone app when dealing with app registrations/logins, go back to the Harmony for all other activity.
Question: is the Roku remote actually WiFi/.11, or is it RF? I long-ago assumed it was RF.
As it stands, I too highly recommend the Harmony 650. I picked that for my parents and set it up for them. It does carry a limitation of only so many devices (five or six, I think), while the more premium models can handle many more devices. I still swear by my own Harmony One.
Eventually, I'll pick up the new Harmony hub-based approach. I love the idea of the cheap keyboard they turned into a Harmony-compatible keyboard remote. I'd use that for my HTPC interaction, and logging into Roku or PS3 or other hardware with apps. I currently use the same keyboard, the one dedicated to PC, and it's functional enough for the HTPC but obviously is limited to said HTPC. Having a universal-remote keyboard on hand, as well as a dedicated universal remote (and smartphone app for when desired) sounds like the best setup, though obviously not the cheapest.