The murder mystery is generally a mystery for four reasons: who did it, how did they do it, how are they caught, and why did they do it.
If you only focus on "who did it", then I believe you have no choice but to accept that the reader is going to try and figure out who did it the whole way. This is because that is the whole purpose of your story. You've set the question, "Who did it?", and the reader wants it answered, so it's natural for them to try figure out the answer to that question. This happens in all books to a degree: how will the protagonist succeed? Will he overcome this obstacle? Will he get the girl in the end? Even if you focus on the how and why, people are likely to second-guess every step of the way that more information comes to light. ("She was having an affair? Maybe he killed him because he found out!")
There are still various ways you can use to get people focused on the story, however.
The most important is through characterisation because this raises other questions that need to be answered, above and beyond the central one of "who did it".
The old "whodunnit" books hardly ever placed their detectives at the centre of the story. They were merely there to solve the crime. There histories were largely immaterial. However, what turned the genre on its head over the years was this idea of the sleuth's life being integral to the story. They're flawed, have conflicts that affect them, and the people around them, they've got baggage they bring to the case, there's political intrigue within the police department, bad relationships with friends, family, ex-lovers.
The story is not just about the crime any more, but the people involved.
The second trick is to have other events operating in conjunction with the crime that add another dimension to the story.
One of the best examples of this (as well as characterisation) that I've seen in recent years was the excellent Danish crime drama "The Killing", which had a murder entwined with a local mayoral election.
A lot of political drama took place that was influenced by the murder (not least because one of the suspects was a politician).
We also followed the family affected by the murder of their daughter, and how their relationships broke down afterwards. We followed the sleuth, whose own obsession was tearing apart the world around her.
It emphasised the point that murders don't happen in vacuums, and they have far-reaching consequences on those involved. It is the impact of these consequences that help the reader become more interested in the story beyond just "who did it". If the only question you've posited is "who did it", that's the only question a reader will try to answer. If you posit other questions, like, "Will he get elected?" "Will she leave him?" "Will he kill the suspect?" "Will she be fired?" then you've given the reader a lot more to be interested in above and beyond the rather clichéd "whodunnit" formula.
Edit: Okay, so based on your comment below, I think you already answered it in your question: play with the conventions of genre, and the reader's expectations. The best way to do this is to immediately destroy a reader's expectation right upfront, because then they're put off-balance, and will know they cannot rely on the conventions of genre for the rest of the story. Make the criminal an early suspect who is released because the sleuth suspects someone else. Make the cops human, so they make errors of judgement, and incorrect assumptions. Make a character appear innocent, reveal that they've lied, or are hiding something, but then reveal that it's unrelated to the case. (The Killing used this to great effect.) Have other suspects who are guilty of something, but not what we think they're guilty of. Create a situation like "the fog of mystery" for the reader, so they cannot rely on what they know from previous works. Of course, that means you yourself need to be knowledgeable about the genre, and that means a lot of reading!