The act of 'gentling' a male channeler (cutting them off from the One Power permanently) is not perceived by the Aes Sedai as using the power as a weapon.
In the books, men can not see the weaves channeled by women, and therefore, Logain would see nothing from Nynaeve's touching of the Source. Also, healing is a complicated process even with the Power, and thus an untrained Nynaeve could not heal to that extent regardless of how powerful she is.