I would say think about how your skin reacts to other things. Do you have a tendency to scar from other things?
I had what the Dr thought was a cyst (actual 'cyst', not acne cyst), removed from my shoulder a few years ago. Once they cut into me it turned out to actually be a ball of old scar tissue. The wound healed fine for about a month, and then overnight it puffed up and I'm left with a keloid scar now (still looks better than it did - don't regret it at all). I bruise easily, get stretch marks easily etc, so I guess I just have delicate or thin skin that's generally going to scar.
However.... my removal was done by a GP with a surgical clinic, not a dermatologist or plastic surgeon or anything. As yours is on your face I'm assuming it would be done by more of a specialist? So that would maybe lessen the risk of scarring?
Personally I would rather have a visible scar than a visible cyst, but everyone is different!
Good luck with whatever you decide!
 

Hello newbie here first let me start by saying Iam grateful for this forum and all the brave souls here sharing their struggle and posting pics thank you .i had a huge cyst which was injected twice and didn't go away I went to two derms whom both said it needed to be surgicaly removed .so this morning that what I did imterrified about the scarring but couldntkeepthat huge bump on my face any longer , both derms said it would keep returning if I didn't remove it .i have stitches now which have to stay in for a week .i got some arnica to help with the healing process I will keep you guys updated .this was my only option after two injection and Cipro nothing helped .i suffered w cystic acne for a long time before biting the bulletand taking accutane I kick myself for not doing it when I first started breaking out but I was scared it def saved my life to me it's s miracle drug however every now and then I do get a cyst but would take it again in a heartbeat .sorry I'm rambling .stay strong and don't give up