I have a feeling they didn't want to get ride of Weir but didn't know what to do with her either because being a great negotiator doesn't come in handy with aliens like the Wraith who are basically part monsters most of the time.
But that's called writers being bad at their jobs. They already did that with Ford and now to do this with Weir? What's the point of writing Weir out of the show just to replace her with Sam who turns into Weir 2.0?