All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His slave and Messenger.
The Prophet, sallallaahu ‘alayhi wa sallam, said: "If people were given whatever they claimed (in disputes), some people would claim the lives and property of others, but the proof must be provided by the claimant, and the oath (of denial) must be taken by the defendant who denies the claim." [Al-Bayhaqi]
The employer's accusation is a mere claim; you have stated that he does not actually have clear-cut proof supporting his claim. This is a mere accusation and it is impermissible for him to withhold the worker's wages unjustly or to cut any sum of it as long as the worker did not confess to stealing or until the employer finds clear evidence supporting his claim. He may refer the case to the court of law if he wishes.
As for the Istikhaarah prayer (guidance-seeking prayer) and the consequent signs, some scholars stated that one of the signs of a positive Istikhaarah is that the person finds himself wholeheartedly inclined to one of the two decisions and feels good about opting for it on one condition: that he does not (insist on) opting for the decision that he had strongly desired before making the Istikhaarah. This is the opinion of Ibn Hajar . Ibn ‘Abd As-Salaam said that one should opt for the choice which is the most readily available, citing as evidence a version of the Hadeeth which reads: "then let him be resolved", and the beginning of the Hadeeth reads: "If one among you wants to do something, he should say ...... [the supplication of Istikhaarah]." Some argue that one should opt for the decision to which his heart is inclined first; however, the Hadeeth in this regard is with a very weak Isnaad (chain of narration).
In any case, the correct opinion is that as long as one has asked Allaah to guide him to the best choice and to keep him from harm, then he will only do that which is best for him even if his heart is not inclined to it. This is the correct opinion in this regard.
Allaah Knows best.