A common alternative of Beta-mercaptoethanol is DTT, but sincerly I don't know if you can use it in this procedure. I can suppose that there are no problems.
I agree, DTT is the only alternative I'm aware of but you might need to modify additional steps in your protocol. I'm not sure it can be used directly in place of it in your current protocol.
Depending on the DNA region of interest I beg to differ. The beta-ME is essential for breaking down disulfide bonds and considering that most studies today look at epigenetics, complex disorders and non-coding regions I would not recommend leaving it out.