We've booked & travelled with Sunshine.co.uk to Malta before now and I've also booked accommodation for my parents with them. Absolutely no problem at all. You even get a letter from a Rep when you arrive at your hotel so you can meet with them - not something that usually comes with booking AO.
We've also used Travel Republic and had no difficulty there either.
I've just reserved 3 rooms in Luxor, Egypt for later this year with Travel Republic and my reservation shows the accommodation is provided by Hotels4U.com which is part of the Thomas Cook group of companies. But, if I book with Hotels4U directly - I have to pay in full whereas now, we've only paid a small deposit of around 20% of the accommodation cost. AND - the prices have gone up since I made my reservation