1)
your wife can apply for conversion from tourist visa to X visa .two main documents are needed for Tourist to X Visa conversions: 1) Submission of a copy of registered Marriage Certificate. 2) Report from the relevant local police station about marital status, including observations, confirmation of living together, and security clearance.
2)
section 5(1) (c) of citizenship act provides that a person can be registered as indian citizen if such a person is married to a citizen of India and is ordinarily resident in India for seven years before making an application for registration.
3)or making an application for registration under section 5(1) (c) applicant has to fill in Form 111 under rule 5(1 )(a)of citizenship rules . if applicant has in preceding 12 months continuously resided in India the said period would be taken into account . further in last 8 years preceding 12 months if applicant has resided in india for not less than 6 years said period would be taken into account .
4) she would not be asked to leave india due to relations with Pakistan