Most esoteric traditions agree that thoughts themselves are not the enemy. On the other hand, when we are thinking, awareness is dulled and confused.

    The vacant state of not thinking of anything
    Is itself the cause of ignorance and confusion.

But there is a thought-free knowing (rigpa) that is totally open like a clear sky that is your own nature. Indescribable, awareness, or knowing (rigpa). Then the wakefulness of knowing your nature will dawn. The difference is like having eyesight and being blind.
Merely recognizing this nature of knowing however is not enough; you must stabilize familiarity with this state. So it is important to sustain a constant remembrance of settling into the natural state.
Shamatha here is being an ongoing steadiness in remembering to settle in the natural state, and vipashyana the recognizing of your essence as natural cognizance.
Mark the degree of progress in this practice by the strength of the luminosity at night.
   — From The Lamp that Dispels Darkness by Mipham