Yes there may be some complications regarding the original booking, especially if she has checked baggage, as if she checks bags in at LHR on her Y ticket, but then "fails to board" in SIN, I imagine that will raise red flags. So I think you would need to call the airline about it, and they may actually refuse to allow you to do this - I'm honestly not sure. Best to call them before booking if you're going to go down that road.
Have you checked whether there is award availability the whole way from LHR-BNE (on the same flights that she's already booked on)? If so, that would be simpler, as she could then simply tell the airline she's not using the return leg of her Y ticket. That wouldn't affect any of the other passengers she is booked to travel with (as they will all have their own tickets, even if they all booked together), and there shouldn't be any fees to pay - she wouldn't get any refund either, but it sounds like you're ok with that.
Getting back to your original suggestion: IMHO, blowing a decent chunk of points and spending a couple of days of your time just to potentially allow her to sit in J on the SIN-BNE sector seems a bit crazy. I'm not sure if you're aware, but a BNE-SIN return in J will cost more KrisFlyer miles (116,000) than a one-way all the way from LHR-SIN-BNE (105,000).
To answer your final question - you can certainly transfer points from your Velocity account to hers and then to KrisFlyer, but that's not necessary. Both Velocity and KrisFlyer allow you to book flights for others (family members in the case of Velocity, and anyone you care to nominate in the case of KrisFlyer). So with either program you can book on behalf of your wife, without transferring points to her. You may also be able to book the flights directly with Velocity points rather than transferring to KrisFlyer.