It really depends on the specific disease and the mechanisms that causes damage to brain cells, but in some cases yes. For most of those disease the toxic compounds will be secreted from the cells, so they are in the extracellular space were the modified cells can take them up and process them.

Gene therapy is not my area of expertise, so someone else might be more up to date on this. The major risk of gene therapy is that the insertion/editing of a gene will lead to unintended disruption of other genes, which worse case scenario might make them more likely to become cancerous. The method used for this treatment, ex vivo gene therapy, were the gene therapy is performed outside of the body is more safe as it allows for extra checks on the cells before they are transplanted back into the patient.