In some part of Autobiography of a Yogi, our dear beloved Yoganandaji is informed by our beloved Paramguru Sri Yukteswar that he may has well strike down a bothersome mosquito, since he already had the thought to do so.
I find myself in situations where i have impulse to act in ways i know are not helpful to my higher Self, yet in some cases i am tempted to behave that way anyway, as if it were my karma. Is it just as bad to think as to act out on the physical plane?
The story you have mentioned from the Autobiography answers your question in the affirmative. For all of us, it is more than a little galling to accept that even the thought we have to take a negative action is very important, regardless of whether we act on it or not!
The intention or thought to harm is where the physical action originates. And so Sri Yukteswar says to Yogananda, “Why didn’t you finish the job?” He then goes on to say that the goal of the practice of ahimsa is to remove the desire to kill.
Arjuna asks essentially the same question of Krishna in the Bhagavad Gita as you have asked.
"Arjuna said: 'O Krishna, by what is one impelled, even against his will, to do wrong, as if (he were being) forced to do so?' And Krishna replied: 'It is desire, it is anger, both of which are impelled by rajoguna. Know these to be mankind’s greatest enemies.'” (BG 3:36,37)
The commentaries on these passages found in The Essence of the Bhagavad Gita are very helpful in understanding what we are up against and how to begin to deal with these energies effectively.
This is also why it is so important that we take up the practice of daily meditation, calming our thoughts and feelings, and spending time attuning to the superconscious state.
Working with the mind and thoughts in meditation is one of the most important spiritual activities we do. It doesn’t matter how perfect we are at doing it, but that we keep practicing daily is vital. Equally important is that we take whatever we gain from each meditation out into our daily activities. It’s very helpful to see each day as yet another opportunity to practice applying that meditative state of consciousness to whatever opportunities we encounter as we move through each day.
Will we be successful at doing this? Well, not if we don’t practice! This is where the great adventure of the spiritual life really begins. As we move forward with courage and joy, the practices of the spiritual life will give us everything we have ever sought from life: bliss eternal, ever-new joy!