Exactly.
The MSM will treat this as "well, if they weren't narrow-minded and homophobic this wouldn't happen. Serves 'em right. They had it coming."
More likely, they will claim it was a member of one of the churches who did it, maybe even a disgruntled pastor (that is the ultimate liberal media dream). They don't get any propaganda value from blaming it on gays.
If they are white churches that were bombed, the MSM will be relatively quiet and the FBI will do little more than a cursory review. However, it is possible that, even if the churches were white and were conducted by some leftist or Satanist crackpots (who, if caught, will only receive minor sentences), these attacks may be used by RINOs to encourage Republican support for "hate crimes" legislation. The argument will be that such legislation is needed because even white evangelicals can be affected by "hate."