No, it will be Harbinger we still encounter at Virmire. Instead of the ominous talk we get with Sovereign, will get Harbinger's song and dance with his taunting. Will get to kill Harbinger, but to elude to Sovereign, the only thing I would have Sovereign take from Harbinger would be at the end before Harbinger dies we get a more calmer, more ominous version of "You have failed. We will find another way." directed at Harbinger.
My problem with this role reversal is that it is thematically dissonant. Mass Effect 1 explores the incompatible and destructive relationship between synthetics and organics, and the conflicting differences between the two forms of life. When Saren is "mechanized", it is treated as something abominable, inhumane. So when we encounter Sovereign, his cold and indifferent emotionless personality echoes that of the Geth and the idea of synthetics we've been fighting all game long, and it's clear why the Geth venerate him as a deity. His ominous and Lovecraftian personality also harkens to our fear of things that are different from us, in this case, machine intelligence.
Come Mass Effect 2, the game begins to suggest through Legion and EDI the idea that perhaps organics and synthetics have more in common than we imagined. The two lifeforms can work together, and are even capable of caring for each other. Now when Shepard is "mechanized" through Project Lazarus, he is still treated with the same respect and love he inspired before; he is "human". For this story, it works that the chief antagonists are in fact entities that embody both the best and worst qualities of both synthetic and organic life. Harbinger's more "organic" personality begins the deconstruction of the Lovecraftian idea, and exemplifies that the lines between the incomprehensible machines and the relatable organics are more blurred than we first thought.