The only reason that there can be a Christian prayer before the meetings, is because it is protected under the First Amendment (per Supreme Court). The real question is that can the Kenai Peninsula Borough decide who is protected by the First? Should they be able to set their own guidelines as to who qualifies or not? Personally, I don't think that should be in their realm of power, and feel that universal standards would be more appropriate in this situation.
I also find it curious that instead of just getting rid of the invocation all together (and I know that was voted on), that they vote to keep it, but also empowerment to determine the source of the invocation. This is clearly a path to discrimination to dissenting views about Christianity.