As soon as you gain control of Batman, grapple up to the ledge just above you, scan the fire alarm on that level and hit it with a batarang, before going up to the top platform and dropping down on the vantage located directly above Penguin. Once both of his thugs have reached the level where you hit the fire alarm, glide kick down onto Penguin and beat him up.
Once he kicks you off, quickly grapple up to the top platform, then destroy the drone with your batarang, before going onto the vantage point at the very top, above the top platform, and disabling the thug that comes up by pulling him with your batclaw.
As soon as you do this, drop down onto the vantage point directly above Penguin, and wait for the remaining thugs to reach the second highest level, before glide kicking Penguin and beating him up for a second time.
Once he kicks you off yet again, simply repeat this last process to finish him off. A few key things to keep in mind during the battle, if things don't go quite as planned: you need to focus on attracting the thugs high up, away from Penguin, to give you enough time to glide kick him and beat him up. Also, if a drone spots you while you're beating Penguin up, it won't stop you, but it will immediately alert the thugs, thus prompting them to come and shoot you off him as quickly as they can.