Unwelcome thoughts while praying? (“Unwelcome” is putting it generously.) This may not be the end of the world. And it need not signal the death of your prayer life – if handled properly.

It is of the nature of inner prayer to reveal the hidden passions concealed in the human heart and to tame them. Inner prayer shows us our captivity to the fallen spirits, making us realize our imprisonment and freeing us from it.

There is no need, then, to be disturbed and perplexed when passions rise up from our fallen nature or when they are spurred on by evil spirits. Since passions are tamed by prayer, when they arise we should practice the Jesus Prayer inwardly, very quietly and without haste: little by little this will allay the up-surging passion. At times the onset of passions and the invasion of hostile thoughts are so powerful that it leads to a great struggle in the soul. This is the time of hidden martyrdom. When assailed by passions and devils, we should proclaim our faith in the Lord by devoting ourselves with the utmost persistence to prayer. This will invariably bring us victory. – St. Ignatii Brianchaninov

Now, whether or not one practices the Jesus Prayer, the principle is the same: one just may, in the course of earnest prayer, have one's hidden passions revealed. St. Ignatii’s advice would then be the same.