Back in the days it was possible to get the VISA without a full wedding. However, everything has changed now and they ask for much more proofs before they issue a VISA. Applicant's who didn't do the rukhsati and applied for PR have received objection letters just like the one your wife has received and to resolve and provide evidence that the marriage is genuine. Applicants have gone back home to do a proper weddding, Walima, and Honeymoon and provided tons of pictures to proove that the marriage is genuine. I am afraid to say but you will have to get the walima and honeymoon done and send as manyctures as possible to avoid delays and god forbid rejection. You can try to write a letter explaining the situation but the embassy is not buying it since high rates of fraud marriages. In addition, you will need to provide what they have asked for, rePCC (becuase the original one is expired) and IMM forms again becuase they want your current and updated work/education/travel history. Also include, upadated emails, phone call logs, money transfer receipt, gift receipts, cards, whatever you can to provide to prove that your relationship is genuine and ongoing. GOOD LUCK Bro!