Obi-Wan is totally outmatched as a duelist. Malgus well before his prime was defeating Aryn, Jedi as fast as Obi-Wan and far more powerful. Prime Malgus was capable of combating Hero of Tython with the aid of Barsen'thor and two greatest non-Sensitive warriors of the Republic.
Hero of Tython alone is combatant superior to Obi-Wan by a whole tier - blitzing Sith warriors superior to Bela Kiwiks, his saber ability trumping Lord Praven way before his prime, with Lord Praven defeating one of the best duelists of the Order at this time. So basically Praven and Obi-Wan are comparable, and you have Hero of Tython superior to Obi-Wan tier even before Chapter 2 of TOR.
Malgus gave a hell of the fight to HoT's superior version supported by equally great Jedi in the person of Barsen'thor, and two of the greatest warriors galaxy ever saw (Smuggler & Trooper). Obi-Wan doesn't stand a chance as a duelist, he will be absolutely crushed by Malgus in a duel.
And let's not even mention Force powers. Malgus was capable of effortlessly choking three members of the strike team at the same time, continuing the lightsaber fight in the meantime. One of them was HoT, who could defend against Vitiate's Force power long enough to prevail with lightsaber. And Malgus was still capable of choking him effortlessly in the meantime of a duel.
Malgus utterly stomps. Darth Caedus vs. Obi-Wan Kenobi would be a closer fight.