This is something I have often thought about myself, albeit in slightly different circumstances because I am a man. When my wife and I separated a couple of years ago, I decided that I would never marry again or even have a serious relationship because my kids were my priority and nothing would come between me and them, I would forsake my own future happiness to protect them.
However, that wasn't the case. I ended up falling in love with my ex g/f and would have done anything to make her happy, and I realised that I could still love my kids and protect them even if things had been different with my ex.
You say that you love your fiance and he loves you. Are you having these doubts out of maternal protection for your kids or because you aren't sure if you really love your fiance? If he really loves you, he will accept your kids and love them too. Sure he won't be their natural father, but that doesnt mean he cant love them as they are part of you and your life.
Regarding their upbringing and maybe even disciplining them, you should have the ultimate say as you are their mother, and I personally would feel uneasy about getting involved in something like that.
The only way you are going to resolve these questions is to have serious heart to heart and be completely honest about your fears and wishes.
If the real reason is that you aren't sure if you do love him and aren't sure about getting married at this time, don't do it. I got married out of obligation, not because I wanted to, looking back it was unfair on both me and my ex-wife and I should have been strong enough to say NO or to ask for a bit more time.
6 months isn't that long to know someone, and if you do need longer, say something before it's too late. If your fiance really does love you, he will understand. He might be a little bit hurt for a while, but he will wait for you if he is genuine, but only providing you are completely honest now.
It's difficult to give advice on something like this as I'm no expert, but my gut instinct would be to follow your heart and not your head.
Whatever you do, do it for you and no one else, dont be pressurised into anything yoyu don't really want.
Good luck