My simple thoughts: SAMs are notably stronger than air-to-air missiles, considerably longer-range, considerably higher rate of fire, but considerably lower chance to hit. Launch off enough, though, and you'll bring down most early-game UFOs. The flip side is that such a high-volume launch draws attention; a line of missiles rather nicely points back to where they came from. Soon you'll have heavy alien combat craft patrolling the areas, and God forbid you take the bait an launch at them when they're close enough to backtrace it for certain.
That's what Interceptors are for. It's harder to backtrace a fighter craft that's had a good deal of room to change course before coming within the UFO's sensor range proper, especially if the interceptor had to do a bit of tailing before closing.
Ideally, in my mind anyways, the interceptors would distract the alien craft, and once the UFO is fixated on engaging or fleeing from the aircraft, a good, hearty long-range launch could do well to soften or bring down the UFO.
I think the alternative function of the SAM sites, once a base has been discovered, would be for resisting landing attempts. Here, obviously, weapon accuracy would also have to take into consideration the size of the target, and the range of the engagement. Firing off a site almost point-blank into a UFO heavy battleship (or equivalent), the player would expect to land a lot, if not most, of the shots. Whether those hits are effective against the pride of the alien invasion force... that's another matter.
...an afterthought: it might be nice, if it isn't too much trouble, to be able to select the number of missiles fired when ordering a launch. It might be more efficient that way, resource-wise, as instead of tracking each individual missile to the target, you'd track it as a single batch, and only worry about the individual hit-miss and damage once the batch reaches the target.
