It seems unlikely that a sensor cleaning would increase digital noise. (Not impossible, just unlikely.) It's more likely that you're just noticing the same amount of noise more now than you were before.
If some sort of fluid were used to clean the lens, it's possible that there could be a residue on the sensor. This would cause general or spotty unsharpness, might leave a color cast, etc., but shouldn't cause digital noise. It's also possible that your antialias filter is scratched - this would probably show up as a line of blurriness across the image. From what I understand, scratching your AA filter is pretty tough.
If you're still concerned, here's how I would double-check:
- Find a high-ISO photo that you took before the sensor cleaning. Preferably, this would be a photo from some place you have access to. (One from your own home would be perfect.)
- Set up your camera the exact same way this old photo was taken. Put your camera in manual exposure mode, and make sure these settings are all the same (They should be available from the EXIF info of the old photo):
- Shutter speed
- Noise reduction
- Image quality (raw vs JPEG high quality vs JPEG low quality.)
- White balance/Color balance.
- Any picture settings, HDR modes, etc.
- Go to where the photo was taken. Replicate the lighting that was used in the photo. If you can't get to where the original photo was taken, find a similarly-lit location. You may need to adjust shutter speed and aperture to get the same exposure as before.
- Take as similar of a photo as you can. Same place, same direction, same zoom. The exact subject of your old photo may not be present (people, etc.) but do the best you can.
Now that you've replicated the photo, load it into the same program you used before (Lightroom, iPhoto, whatever) and apply the same presets and adjustments. If you have the raw file for your old photo, re-process both without noise reduction.
Compare the new photo with the old one. Compare corresponding places from each photograph. Hopefully, they're the same; reassure yourself that the increase in noise is just in your mind. If they're different, call Canon, present the evidence you've just collected, and hopefully they'll fix or replace your camera for free. Then, of course, post the evidence here.