As long as your wife entered the country legally (which she did), she is eligible to apply for lawful permanent residency (green card) based on her marriage to you assuming you are a citizen. The overstay on the 90 day visa waiver is irrelevant as long as you were married after she was here for 60 days or more. There is no limitation on the amount of time you need to wait to file for her green card if the visa waiver has expired. Unfortunately there is no way to extend a visa waiver, so you should submit the application as soon as possible.
As far as taxes are concerned, you should be fine to go ahead and file. Make sure you indicate that you are married, whether you file jointly or separately. You can use your wife's ITIN for tax purposes. This may have tax consequences, but if you are married and submitting the proper immigration documents, the drawbacks end there.
I would agree that $5000 is a bit steep for a marriage-based adjustment, but fees do vary from location to location and from law firm to law firm. My advice would be to shop around.
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