Maybe you won't have time to get over to the Hebrides but if you did and had only one island to go to, Harris would be a good choice. Beautiful island and if churches are your thing, St Clement's Church at Rodel is an interesting place to visit:-

http://en.wikipedia.org/wiki/St_Clement's_Church,_Rodel

http://www.scotland-inverness.co.uk/rodel.htm

It doesn't take long on the ferry from Harris to Berneray which opens up the Uists to you, or alternatively it's not a long drive from southern Harris up to Lewis where the likes of Callanish is situated.

I often think Skye is over-rated and personally prefer Mull, which of course also opens up Iona to you. The last I was there I stayed just a mile or so from Dervaig where the church with the round spire is situated. A great place to stay there is at Druimnacroish :-

http://www.druimnacroish.co.uk/