Took away baby's pacifier, now fights bedtime?

I have an almost 2 year old. I took away her pacifier almost 4 weeks ago and she still hates going to bed for either naps or nighttime. I put her in her crib, she refuses to lie down so I just say "sleep well" and leave the room. Then she wails, cries and complains for 2-5 minutes tops, then quiets down and sleeps well. She sleeps well yes, but it sucks that it's no longer a happy experience putting her "down" (quotation marks cause she's always standing up when I close her door). My questions are: have you experienced this? When will it go back to happy bedtimes?