It becomes pretty simple how the Autobots got rid of the Allspark with Sentinel Prime's space bridge pillars. The plan likely was get the Allspark out of the Decepticon's reach and pick it up after they've won the war. That's just it they weren't winning the war. The Autobots were finding themselves outnumbered and outgunned. Besides Megatron's own CONvert forces the Fallen likely added his own troops to the war. The only guy who had an inkling of how to find the Allspark was Sentinel Prime and the Autobots thought he blew up with the Ark. With him the chances of finding the Allspark and the ability to reconnoiter on other planets. Of course they didn't know Sentinel Prime made a deal with Megatron telling him where the Allspark was headed.