Before Ser Barristan came along, Ser Jorah was Dany's most trusted advisor. This position was well deserved BECAUSE, despite his past of informing on her, he demonstrated his devotion by saving her life, and giving good counsel consistently, despite the opportunity granted for him to go home.
Barristan is a good warrior, certainly suitable as her guard, and with his presence beside her many who would have denied her at first will now be more accepting of her as queen in westeros. However, Barristan has been institutionalized as Kingsguard and doesn't know how to think outside the box of his oaths and honor, and if his advice were taken, Dany would never have acquired her unsullied, would have gone back to Illyrio, probably married aegon and would have had no ability to exercise her own will as she would be a queen by name, not by power, as she would have accomplished nothing but providing the dragons.
Varys probably didn't expect Jorah's allegiance to swing as far as it did toward Dany. It would seem perfectly reasonable that Jorah would not only accept the pardon, but maybe even try to claim the lordship for himself, being as close to her as he was. It was probably a twist in the plans for him to choose a horse from Drogo as his reward instead and remain in exile, as his letters became more few and far between then eventually stopping all together. In the show we see one of Varys "little birds" inform Barristan of Jorah's pardon, though we know from the books that Varys, "supports" Danny. Could be that the reason Illyrio sent Belwas and Barristan in the books was to divide her from the only counsel she has had so far that got her anywhere she is now? Barristan didn't have to KNOW that he was being used like that, but it seems apparent that based on the information he learned at the small council from Varys, that he would do everything to get Dany from the closest threat she doesn't even recognize, without realizing that the real threat was himself.
Without Jorah around to guide her she has been unable to move forward because there is no creative strategy, and she would become dependent upon the aid of Illyrio, and by association Aegon, so her Dragons can be used for his conquest of the seven kingdoms. He who holds the king holds the kingdom, well Illyrio and/or Varys are still trying to get the rightful queen firmly into their grasp.