I would tend to agree with Kerby that it would be best to relocate the snake a good distance (but not too far) from your home if this can be done safely. If not, you might consider getting in touch with someone who feels more comfortable doing it.
As far as the backyard ecosystem, I doubt it would have much of an impact. I have gone herping in fairly populated areas of Northern Arizona (Prescott and surrounding) and never failed to find several different rattlesnake species in relative abundance within a few square miles. So if you live in a rural area I would bet that your Crotalus population is pretty stable. Plus there are plenty of rodent eating colubrids around.