Yes, you can actually complete most quest steps even after taking down malenia - just keep track of the specific timing windows. Millicent will still appear at her regular spots and you'll be able to help her against those invaders near the prayer room, which triggers right when you spot her there. The fight itself has some tricky positioning but stick close to millicent's summon sign, and focus on drawing aggro from the sisters while she handles the rest. After winning, you'll get the rotten winged sword insignia, though timing is important here since you won't be able to use the unalloyed gold needle on malenia's bloom anymore if you've already defeated her.

Just remember to exhaust all dialogue options with millicent, as her responses change slightly depending on where you are in the questline progression. The one thing you absolutely can't get anymore is miquella's needle, since that requires interacting with the bloom right after malenia falls but everything else in her story remains totally doable including all the key items and narrative beats.