For your best friend, I think that you should grin and bear it. Head tables are very common and spouses should be able to sit apart for a couple hours max. Your friend may be very hurt your husband skips her wedding b/c he doesn't want to sit with people he doesn't know for the dinner period.
This topic has come up here several times before. It gets very heated because some feel as you do - they don't like being apart from their spouse. However, true etiquette states at dinner parties/receptions, spouses not be seated together so as to promote conversation with others around the table.
If this is a deal breaker for you, then decline being in her wedding party. Otherwise, if you say anything about not wanting to sit at the head table, it could cause a rift. She already has plans for a head table, which is pretty standard and traditional, and being a dissenter may add stress to her she doesn't need. It really is only for a couple hours, a very small amount of time on your best friend's wedding day.