I got a quest early in the game where som old lady wants me to posion som potion that a gang is making.

I want to do all quests since I am a completionist but the quest descript says that It will also kill civilians... if I do this kind of optional quests can I still get the good ending or do I have to wait until my dark ending playtrough to do them?

Just watch your chaos level at the end of every mission and keep it at low.

For a good ending, you want to make sure your Chaos level is "Low" which you should be able to do while still completing all the (main and side) missions in the game.

No one act will set you into "High" chaos, so as long as you're not running around doing reckless murder you should be fine. Keep your kills to a minimum.