I have 2 PVR's (non-Tivo Personal Video Recorders w/Hard Disks), my new one has an IR Blaster so that one is no problem and so far Comacast as only gone QAM on a few channels but over time will got to all, they are giving the converter away for free t oavoid the issue you mention.
In any event given the cost of the second converter box was only 6 bucks a month, I kept my old box, and Comcast has a feature where you can tell it to tune to a station on a set date/time and it does, so for the PVR I have that has no IR Blaster, I just use the cable programming feature.
As for my main TV, since the few channels that Comcast has changed I really don't watch I have my PVR hooked up both ways, an S-Video to the cable box for scrambled channels and those record through Input 1 and for the other channels with just the out of the wall cable, I program it through the PVR EPG, life is good. The PVR I have lets me pick the input source on a per channel basis. Since the cable programming option is not actually a function of the converter box itself but is controlled by Comcast, I do the same on it for setting digital channels my PVR can't process scrambled or not.
My main TV also has many input options, a QAM tuner so I still have that plugged into the wall as well as the HDMI input from the cable box and the component output from the cable box goes to my HT so I can upscale or upconvert.
So I have options out of kazooo. For casual TV watching, which for me is "flipping" and watching parts of several shows at once cutting between them during boring parts or commercials, you can't beat the speed of flipping from my TV which is why I like to use its tuner, the cable box making flipping painful, the TV just flies from channel to channel, I have no idea why cable boxes are so slow on channel changes...
In any event, until I cobble together my HTPC, my latest project, I am well covered now. Putting together a HTPC that with a QAM tuner(s), a Blu-Ray recorder, regular DVD/CD recorder is not really all that hard. The part I can't get is that total easy of use of the dedicated PVR's that dropped from the US markets last year. They are alive and well in Europe, Asia, Aisa-Pacific, but totally dead in the US markets so far, so my prject is to replicate in a PC with a A/V component footprint a PVR and the only missing piece is this highly integrated software that made it so easy to use, that I suspect that will come in time as more people take an interest in HTPC's, in the last year I have seen off-the-shelf units go from a few choices to a dozen or more, only time will tell how far that market will go, there is a limited demographic for it now.