Barry and Co. were vehemently against the idea of killing The Thinker as recently as last week.
The Thinker wears his Thinking Cap often on The Flash; if the good guys are somehow able to overload it with dark matter, it would enable them to incapacitate him without killing him.
Sparing his life might make Team Flash feel better; zapping his brain could be much, much worse for him.
If the priority is to be merciful as heroes, zapping his brain could be the worst thing they could possibly do.