A scratch on the focusing screen won't affect Auto Focus at all, since the light used for AF, whether phase detection or contrast detection, doesn't pass through the focusing screen. It will only affect what you see through the viewfinder. If severe enough it might affect metering, which does use light that passes through the focusing screen. But a single scratch probably will have no effect on metering.
There are third party vendors that offer aftermarket focusing screens for the 7D. Note that depending on the particular screen you may need to use exposure compensation to correct for the different amounts of light each screen allows to pass through to the light meter. The KatzEye with the optional OptiBrite treatment gets good reviews and doesn't seem to affect metering very much, if at all. They also offer to install it for you for an additional charge. I've read reports on discussion boards that if you combine the screen + OptiBrite + factory installation in one purchase they'll apply a discount that brings it to about $200 + shipping. I've seen other discussions that say as long as you have the correct screwdriver (a cross "000") it isn't that hard to do yourself which will run you about $160 + shipping. Be aware the translucent LCD for all the viewfinder overlays is just below the focusing screen and you don't want to move or disturb that! YMMV.
There are a couple of small sellers on amazon marketplace that claim to sell the genuine 7D focus screen, but I would be wary since Canon does not appear to make it available to the general public. As far as sending it to Canon factory service I have seen anecdotal stories ranging from no charge (usually fairly new and certainly still in warranty) to included with a viewfinder and sensor cleaning at a Canon SC ($60+GST in Canada), to the more typical "Level 1" tiered rate structure used by Canon Service Centers (all "Level 1" repairs are a set price, all "Level 2" repairs are the next higher set price, and so on).
