You can counter her FIR if her(assuming you charged under 498A) statement said to be false and you have some evidence;
You have to prove your innocence in Criminal cases and in Civil matters you defend when case is running but to file Damage / Defamation you have to have Final verdict on your case.
You can file suit for damages for malicious prosecution.You can also file criminal complaint for defamation.
Malicious Prosecution: victim needs to prove his innocense. ( eg: 498A IPC )
1- he was prosecuted by defendant - Where the magistrate takes cognizance of a complainant under s.190 of the Cr.P.C, examines the complainant on oath under s.200, holds an inquiry in open court under s.202 which the plaintiff attends and dismisses the complaint under s.203 of the Code, the prosecution is deemed to have commenced so as to found an action for malicious prosecution (bar under s.195).
2- proceedings are terminated in favour of plaintiff - Even if plaintiff is convicted by trial court and on appeal is acquitted - cause of action for malicious prosecution arises. Plaintiff (accused in 498a) need not prove his innocence but merely absence of any judicial determination of guilt.
3- reasonable and probable cause - your wife should honestly believe and that belief must have an honest conviction of the existence of circumstances and these circumstances should be reasonable grounds which would lead a fairly cautious man in your probable guilt in order to file a case against you.
4- malicious intention and damage to reputation should have occured - wish to injure you rather than vindicate by law, absence of reasonable and probable cause, proof of absence of honest belief, false charges, acquittal on merits and not merely acquittal.
Also, judgment of acquittal in criminal proceedings is evidence but not enough in civil proceedings - you need to discharge the burden of proving want of reasonable and probable cause (wife had no cause but was done out of malice) for the prosecution - for recovery of damages.
Read more on defamation here http://mynation.net/ipc4.htm