I found Malek pretty tough as well. It took me three tries to kill him. I stock piled lots of energy shields and healing packs, and used my force powers to heal me as well. Ultimately, you need to somehow stop him from attacking you whilst you kill the entrapped Jedi. I just ran as quickly as possible

Once the Jedi are dead, its really just a case of using as many healing/adrenaline packs as possible, and keep your shields going. To be honest, I don't think it will be very easy at all to kill him without a lightsaber because you need to be able to parry some of his attacks.