I'm afraid you won't find what you want for a number of reasons. So you need to either modify your expectations or change your budget significantly. Here's a breakdown of why; and I've changed the order of the point you raise to tackle some of the biggest issues first...
I need a receiver with at least 3/4hdmi inputs, I was shocked to find that a lot of receivers still only have like 2 hdmi inputs
That's because I think you're looking at all-in-one kits along these sort of lines. It's a kit that comes with built-in BD player and speakers. That's where you're going wrong
If you look at proper AV Receivers, where the main unit is just an amplifier with radio tuner (the definition of a "Receiver") then even the most inexpensive branded products come with 4 HDMI inputs typically. You then buy the Blu-ray player and the speaker kit to go with it. This type of system is know as an AV Separates system.
the two speakers either side of the tv need to be free standing for ease of use
This is something common with all-in-one kits but not so much in your £150-£250 budget range.
also I require a receiver that allows me to turn off/lower the volume/mute specific speakers if thats at all possible, basically turning a 5.1 into a 2.0 setup, this is for late at night where I want the rear two to simply act as normal 2.0 speakers with all audio coming out of them when I cant have the surround sound on too loud, I hope this is possible as if it isnt, it should be as I think it'd be a very useful feature.
I understand what you want but I'm afraid this doesn't exist in any AV amp I've ever come across up to £3,000 let alone under £250. The only way to achieve this would be with quite a complex speaker switching box that would reroute the signals to the various speakers. The cost of such a box alone could easily be more than you want to spend on an entire system.
To cope with late night use there is Night Mode which operates on Dolby Digital, DTS and HD Audio sources. This decreases the dynamic range as part of the digital decoding process. That's okay for your movies off disc. For TV viewing where the source is stereo or ProLogic (a basic form of enhanced-for-surround stereo) then you can force the amp in to stereo mode rather than the default 5.1 surround, or you can use 'all channel stereo' mode which will do what it says on the tin. That way you can reduce the overall volume and still have a stereo signal on the rear speakers which would be close by you. Alternatively, invest in some headphones.
To get what you want in terms of HDMI inputs and tower speakers at the front then your
minimum spend on an AV separates system would be:
£100 on a Pioneer VSX322 or Sony STRDH520 AV Receiver
£50 on a basic LG or Toshiba Blu-ray player
£300 on the Tannoy HTS201 speaker system
and roughly £50-£80 for interconnects and speaker cable.
Total spend approx £550-£580.
I think you'll have to search long an hard to find an all-in-one BD home cinema kit with more than 3 HDMI inputs. I had a look at the top-of-the-range Samsung (HT-F9750W £1499.00 @ John Lewis) That has 2 physical HDMI inputs + the ARC feature which they count as a third, but it does depend on your TV being ARC compatible.