Malaysian nationals indeed do not require a visa if their stay does not exceed 90 days, if the purpose of the visit is tourism, on missions, business, invitations, ought to take part in sports events, or study. However, your wife should apply for a Type-D long-term visa (Visto Nazionale) since the purpose of her visit is effectively to accompany you (her non-EU spouse) for 6 months:
- Long sojourn or "national" Visas (NV), which are only valid for visits that are longer than 90 days (type D), with one or more entries, in the territory of the Schengen State whose diplomatic mission issued the visa. Holders of type D visas are permitted to circulate freely in Schengen countries other than the issuing one for a period of not more than 90 days per half-year and only if the visa is valid.
She will then need to register for a residency permit (Permesso di Soggiorno) no later than 8 days after her entry in Italy. Quoting from this last website:
Non-EU citizens in possession of a National Visa (NV) for sojourns longer than 90 days are required, within eight (8) days from entry into Italy to request a residence permit (permesso di soggiorno) from the Italian authorities, and will be subject to photo/fingerprint registration.
Only this residence permit, which is issued for the reason and for the period indicated on the visa, authorises an alien to sojourn in Italy.
Since the Permesso di Soggiorno is not issued to visitors on Type-C short-term visas (for sojourns not exceeding 90 days), it should be safe to assume it shouldn't be possible to apply for one after entering Italy on one such visa. Moreover I would avoid trying to do this, since your wife would effectively be violating the EC Regulation on Visas, by entering the Schengen area for purposes not covered by her issued visa (long-term stay on a Type-C visa).