Here's what I'm seeing:
Your metamour had an unplanned-for need/desire (to not be alone) and asked for what she needed. Poly-points to her for knowing what she wants and asking for it. (Not that we're keeping score; just go with me here.)
You heard her and worked with your husband to meet her need on the fly. Poly-points to both of you, plus bonus points for flexibility and graciousness, and bonus bonus points for offering the guest room.
Everyone's needs are met and all is cool in the land of poly until her need for company (now satisfied) bumps into your need for privacy. It seems to me you simply found the outer edge of your ability to accommodate her need, and need to get comfortable expressing that to her. When you know her better, your comfort level around this kind of situation will improve. Until that happens, I hope your husband will help bridge the gap.