IF the only problem is that one of the IR blasters is out then replacing that blaster is pretty simple.
IF the original installer just used an IR extension system that has an IR receiver in each room and a IR emitter for each box you will still need to fix the blaster even if you change the remotes to the Harmony using IR.
If you want to eliminate the old IR setup then I don't think you can do this with the Harmony remote since the RF extender that they make doesn't allow for IR routing to the correct Direct TV box; hey all use the same codes so you have to route the IR to the box that is working with the TV you are watching. I don't think you can use multiple RF extenders either unless they have the ability to link them only to one specific remote and not the other four that would be operating on the same band.
You could use one of the URC custom programmed remotes since their RF to IR extender allow routing to the IR port you have assigned to that DTV box.
With these you can make the TV commands work in IR and the DTV box codes work in RF.