1) since you entered into agreement with builder to purchase flat in joint names sale deed would be regd in your joint names
2) only if your wife writes to builder to register flat in your name alone supported by affidavit wound builder agree to register flat in your name alone
3) if loan amount is not disbursed cancel the agreement with builder and inform the bank that you don't want the loan . At most builder will forfeit some portion of your earnest money paid