Your MR is over. Sorry to be blunt Paco, but you seem to be in denial about that one, simple fact.
Even if you end up back together, it has to be in MR 2.0, with a new dynamic. So you need to start thinking about it in those terms. Your M is over.
Now, some good news. D doesn't mean no R (AS and I just had this conversation with another poster!) Sometimes D has to happen for R to occur later. Maybe R will never occur. All of that is OUT OF YOUR CONTROL. So stop trying to control that.
So let deal with this question:
"How am I supposed to approach this situation when I know it will lead to conflict but I do not want to start divorce and I want to transmit to her that I love her and that I want to fight for our marriage but not at any cost?"
First, why are you afraid of D? Fear is never going to help you move forward. And you speak about all of these things as if they are mutually-exclusive. They are not.
You can fight for a better separation agreement. First, hire a lawyer. These are legal proceedings and you need an expert to guide through it. Take the agreement to a good D attorney, and let them craft an agreement from it that you can live with. Then have your lawyer send it to her. With an official agreement from a law firm it will carry more weight.
Second, in any interaction involving the kids (drop off, pick up, communications about drop off and pick up) be upbeat. Kind. Pleased. Content. That is how you show her you are changing. That is how you "transmit love". You also transmit love by giving her the space she wants. At this point you should be No Contact. I know your next question is "what about the kids?" NC means no contact UNLESS it is about the kids.
Here is how it works:
All communication you initiate is about the kids...and the kids only.
If she initiates contact about the kids, engage. If she initiates contact not about the kids, you listen and validate (if verbal).
If she texts or uses written communication and it isn't about the kids, you do not respond unless it is a direct question. If it is a question you answer in your own time (not right away), and then in as few words as possible. Yes or no questions should get yes or no answers. If they are difficult questions like "Did you sign the separation agreement yet?" you redirect. "Sorry, been really busy. I will need some time to digest the agreement before I respond."
You have to drop your fear of D, start handling her in a business like manner, and only engage her when it is about the kids, and even then do so business like.
Paco, if you want to save your marriage you have to STOP trying to save your marriage. See this thread: