Just my take...
So much of this case is elusive, bizarre, odd and yet so very black and white. We see everything but the obvious which is the reality that no one really knew Gareth Williams, not even his own family it would seem. One young man who knew him as a young boy described him as being naive, but goes on to say he didn't really know GW.
Who was this man? What do we know about him? Absolutely know, not what's been in the news. We know for certain who he worked for, was missing for 7 days before MI6 reported him missing. We know he was one of the best hackers in the world who just so happened to be employed by his government. He wasn't happy working with MI6, he wanted to move back to the countryside. He had no close friends, lovers, male or female, if he had they'd have already come forward for that 5 seconds of fame. We know he was found in a duffel bag, naked but not bound and that it was locked from the outside. We know that his apartment was locked and the heat was turned up excessively high so as to aid decomposition.
After all of that what we know gets spun off into a million different directions including some pretty bizarre ones. The story his former landlady told about him tying himself up was pretty predictable given that she just basically regurgitated some news story but embellished a bit having to play the part of the rescuing party. But by her attempting such a poorly drawn out story, she unwittingly gave a small measure of insight about GW. No it's not sexual, it's that she may have viewed him as weak, innocent, naive or just simply careless.
Let's be honest, no government wants to admit they employ sexual deviants, traitors, liars, abusers and killers. The fact is that they do. That leaves us with one of three choices:
1. GW's death was accidental, resulting from a bizarre sexual encounter, either alone or with guests. Possible but not likely because at the beginning of the case his former landlady who adored him, before she hopped on the 5 minutes of fame train stated that he never partied, had guests over, never kept odd hours.
2. GW found intelligence that he could sell. A little more likely, but it's doubtful given the fact that he seemed to find it difficult to make friends, in order to sell intelligence one would need to form some type of trusting relationship with his buyer.
3. GW was assigned to gather intelligence on a fellow spy who might have been involved in something he shouldn't have been or a fellow co-worker at MI6 ratted him out to another agency. The last time I checked, spies do spy on each other, they kill each other sometimes over very little. So yes I believe it was an inside job. But by whom and exactly how inside only MI6 knows. More often than not these agencies have several layers, more than we the public are privy to, more than agents are even aware of.