My MLCer told me that separating gives us the best chance for staying together.
Sounds ironic, doesn’t it? The best chance to be together is to not be together. As with many things, some MLCers mean this and others are using it to placate you and as their excuse to leave. If the words are genuine, your MLCer has an inappropriate motivation for separating. He wants to find out if he misses you. How then will he interpret his feelings for you when he does not miss you because his depression keeps his focus inward on himself and his woe is me problems? Instead of considering that he is simply preoccupied, he will likely interpret his lack of emotion for a lack of love and care.
Is it true; does separation offer the best chance of reconciliation? In non-MLC situations I’ve read that it is not true; separation has a greater likelihood of ending in divorce. But in MLC it doesn’t matter. I don’t mean that the odds are the same either way, I mean it doesn’t matter if your MLCer is going to leave, regardless of statistical odds about separation; most leave. That doesn’t mean that they do or do not return, but most will leave. It’s not that separating offers you a better or worse chance for being together in the future; it’s that it will happen anyway and it is not for you to stop it.

I told him I don’t know if I can take him back. I can’t make a guarantee; I don’t know how I’ll feel once he’s gone.
Is this an honest statement or are you trying to manipulate your MLCer into staying? This is not Standing; it is clinging and living in fear. You are avoiding and denying for the same reason that so many couples avoid counseling until so much damage is done that the counselor is ineffective or they see lawyers instead of a counselor. Such couples are afraid they will learn in counseling that they should not be together. What an irony, they want to be together so they avoid marriage improvement sessions because they think it will damage their marriage when they learn the truth. What if you feel great once he’s gone? That is what you are afraid of—that you will appreciate and enjoy your life better without him in it. If that is true, what’s wrong with it?
I’m a Stander, I do not believe in divorce, but I do believe you have to ask yourself and answer the tough questions. I have no problem admitting that when Sweetheart left I felt relief. I was more relaxed and choosing joy became easier. I no longer had to worry about which mood was coming home at night and what new taunts he had planned for me. I no longer had to feel as though the responsibility for boosting his depression belonged to me and I no longer had to deal with his criticisms and complaints. When he was gone, life was more enjoyable because instead of tending to him I was able to focus more consistently on my Self; that did not mean I wanted him gone permanently. Living with Sweetheart is enjoyable; living with the MLC Monster is horrible.
Your MLCer needs to feel safe; your fear is preventing this. You are clinging to your marriage because you are unable to commit—ironic isn’t it? Your MLCer needs space to explore and find Self and uses the word separation to explain and represent this space. He wants the space but avoids actively trying to seek it because he fears that if he does you will not be there when he is through. What you have are two people who are so afraid they will not like each other tomorrow that they would rather remain frozen in a loop of Time clinging to each other in misery today.

But I can’t give him permission to go.
Remember your language. It is okay to refuse permission—he doesn’t need it. But you are choosing, therefore the proper term is won’t; you won’t tell him it is okay to leave. Changing your language is about taking responsibility for your choices and actions. It is okay to refuse to agree or give permission; he doesn’t need your permission. Accepting his choice does not make it an endorsement.