He didn't send Maul to eliminate the two Jedi just to have a lightsaber battle...he wanted them eliminated because they were investigating the blockade and becoming close to exposing who was behind. Or at least he feared that result.
They were investigating the blockade? Since when? I thought at that point their goal was to capture the viceroy? Why would Palpatine care if this happens or not? The viceroy had no idea who he was, clearly, as when he was captured the Jedi still had no clue who was behind it all..