Yes, she can travel with you. Just be sure to bring a copy of your marriage certificate.
She should not attempt to enter the Schengen area without you unless one of the following is true:
- She is traveling to join you in the Schengen area, or
- She has not reached 90 days in the Schengen area during the previous 180 days, or
- She has a valid carte de séjour.
This is governed by Directive 2004/38/EC. This outlines three rights:
- The right to enter (Article 5):
Without prejudice to the provisions on travel documents applicable to national border controls, Member States shall grant Union citizens leave to enter their territory with a valid identity card or passport and shall grant family members who are not nationals of a Member State leave to enter their territory with a valid passport.
- The right to remain for up to three months (Article 6):
Union citizens shall have the right of residence on the territory of another Member State for a period of up to three months without any conditions or any formalities other than the requirement to hold a valid identity card or passport.
The provisions of paragraph 1 shall also apply to family members in possession of a valid passport who are not nationals of a Member State, accompanying or joining the Union citizen.
So, when your wife is with you, she can remain up to three months in each EU country. This doesn't, strictly speaking, apply to your home country, but it is unlikely to be a problem, especially if she has the receipt showing that her application for a carte de séjour is pending.
Once she has her carte de séjour, because it counts as a "residence permit" under the Schengen codes, she can also travel alone throughout the Schengen area, subject to the 90/180 rule, in addition to being able to travel with you in the EU, subject to directive 2004/38/EC.
The interplay between the Schengen rules and the directive can be somewhat complicated, but in practice you will almost certainly find that the fact that you are married and traveling together will be enough.