My take on this is that Shar knew about the prism, but simply just did not care. Sharran documents like to refer to the Dead Three as “godlings” which makes a lot of sense from the perspective of Shar. She’s old. Like really old. To her the Dead Three are not much more than mortals who tricked their way into a fractional amount of power, so their machinations are childlike at best and nowhere near on the scope of what Shar is capable of.

I agree though that Shar wouldn’t thematically ever make any personal appearance or have any direct involvement with any of her plots. That isn’t her style. She would whisper commands to super high level followers, but even then never divulge the why of it. You would just get orders not explanations.

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My interpretation was that Shar had nothing to do with it, it was Mother Superior making a power play. If you have Shadowheart kill the Nightsong, Shar empowers her to “cleanse” the church of the unfaithful (meaning Mother Superior and her acolytes).