Yeah i would, poipet really wasnt a pleasant experience. It was so easy and quick at the southern border. I wouldnt do your visa run from samet or chang. I would stay one night in maybe trat or rayong on the mainland and then head to one of the islands after you have got your visa. Just baring in mind the extra costs and hassles of boat journeys to and from the islands.
Koh samet- buy a boat ticket that takes you to the pier at the north of the island...from here get a taxi (pick up truck) to the beach of your choice (you will have to pay about 250 baht when you arrive as it is a national park). We chose to stay on the beach closest to the pier (sai kaew beach)- simply because we stumbled across some really unique accomodation and its right near the village (the best internet connections, seven eleven etc etc is all down this end of the island). We stayed at 'sinsamut' and because we agreed to stay over 3 nights the lady discounted our rooms. I think we paid 500 baht a night for our room...but they were slightly different from your average huts (they were little log cabins, set in a pretty little garden...own hot shower, flushing loo etc). Also next door is saikaew villa's which is also very good accomodation.
If you want cheaper accomodation, head further south to beaches like au phai, au phutsa and au cho. I think toks, naga and Jeps on au phai beach have fairly cheap rooms...prob more like 400 baht but i dont think they are as nice. Bare in mind it only takes half an hour to walk right down to the fifth beach on the island so it might be worth one of you staying at a bar or somewhere with your bags whilst the other person just walks along the beach and chooses some accomodation.
Oh and go to Jeps restaurant for some quality food. Its a little more expensive but lush. And if you like a drink or two make sure you play toss a coin at naga, toks and silver sands bars...if you win the toss you get a free drink, if you loose you just pay the normal price!
Have fun, i wish i was still there myself!