It is a good day - I'm going fishing!
The BL5s are clever in that they detect signals, whether from Line-In or the coax s/pdif. They give priority to the s/pdif, if detected. Which means that you can have two different sources connected to the speakers.
If you have more digital sources than one, then you have a challenge, but it's easily solved.
A simple solution would be to get a CD-player that has digital inputs. Cambridge Audio has an excellent one in the 840C Azur. This gives you optical and coax s/pdif IN, in addition to your being able to play CDs. In other words, three digital sources, all connected through one cable to the BL5s.
If the Cambridge Azur 840C is too inexpensive (), you can get the same functionality and sound from the substantially more expensive dCS Puccini.
But if you're also playing surround sources, or very high resolution sources, then this solution won't do.
You quite correctly identify the sampling issue with the BeoLab 5s. They work at 24-bit/96kHz; they do not understand a surround digital signal, it has to be processed before it reaches them. But they will accept any analog signal, and process it as a pass-through signal.
So to solve that potential problem - with sound sources in resolutions in excess of 24/96 or non-native (digital surround), you just need to get it properly processed before it reaches the speaker.
This you can do with an A/V receiver or preferably A/V pre-amp, with analog 7.1 pre outs. (You don't need an amplifier, since you have that in the speakers).
There are a variety to choose from, and you'd probably want to consider one that matches your other components when it comes to remote control.
You'd want one that processes HDMI, various digital signals and other sources - and which outputs a pre-amp signal to analog 7.1, correctly decoded. Some allow for volume-control through the unit.
You would connect the BL5s to the pre-amp using LINE IN on the speakers. Make sure the pre-amp allows you to define "No center speaker" - the BL5s create a brilliant phantom centre, and it must also allow you to send the low frequency (sub woofer signal) to the front speakers. Some pre-amps also have digital OUT, and for the signals that are appropriate, you might want to have that connected to the speakers, if you don't go for a separate as described above (the CD-player with digital IN and OUT).
As to which specific A/V pre-amp that is suitable, that depends on your other components and requirements. But there are a number of very nice units on the market now.