Plus - even if they were, it would only be (arguably) inconsistent if Apple were refusing to do business in Indiana. It would only be hypocritical if Tim Cook were, himself, discriminating against gays. The actual meaning of "hypocrisy" appears to have been lost in the excitement of the religious outrage.
Perhaps an oversimplification - the Presidency is a crappy job, but many people simply aspire to positions of authority, of which this is one of the pinnacles. The best candidate is one who does it from the motivation of civic duty, and such a candidate obviously has to pursue it at some level. Pursuit of the position, for the right reason, should not be an automatic negative.
There is certainly a case to be made regarding the distinction between simple service and participation. One should probably not be required to participate in a private event that one disagrees with or finds distasteful.
I think that they are only trying to appropriate the rights and benefits that are accorded to the institution of marriage. The fact, that in a secular country civil marriage has become intimately convolved with the religious meaning, is hardly their fault.