I feel like people are a little too paranoid about Lobotomy, it never did anything we didn't want it to, the description explicitly points out that it does do what we want perfectly as we want it, and while it can be used for mind control, this isn't what we're using it for.
It is a helpful tool to help with discussing and stabilizing mental health, just like any tool, fearing how it can be misused is worthless when you are the only one with access to it and have no intentions of misusing it.
Plus, helping manifest EGO can help X too, show her that she can actually do more than distort those around her, that the Light can do what it was created for, that her job was not pointless.
Sure training Sayaka can do things for her, but we can still have her do so after she get her own EGO, it's not like she wouldn't benefits from it, and with EGO, we can include Madoka in the training after helping her manifest it too.
We are a representation of the seed of light, of all the blood and tears that were drawn out with the singular goal of giving EGO to the world, and we decide to hide every time we could do so? Refuse to help people get better in a tangible way out of, I don't know, shame? Fear?
We can do better for Sayaka, we can help her be the best Sayaka she can be, we can help her cristallise her dream, reason with her to help her go trough her feelings, show to her that she's not an impostor, she's Sayaka, and she doesn't need to be anyone else.
We can have her show to the world the beauty of her heart and mind, soar like Xiao did when manifesting her own EGO, make her special just like she asked us, and we can offer the same to Madoka, make her feel helpful, make her able to really defend herself, make her independent.
We just need to trust in ourself, stop being controlled by this fear of failing, spread our wings far and wide with pride, instead of confining them to being nothing but basic diagnosis tools, show our own potential and draw out others.
Edit:
Or, in short:
[X] offer to help Sayaka manifest EGO…
-[x] Over time