Malthouse took over when Brett Ratten was removed at the end of 2012 and helped the Blues sneak into the finals in his first season at the helm, when they replaced disqualified Essendon in the top eight.
But Malthouse lasted only another 30 games - for eight wins - before he was shown the door in May 2015, bringing down the curtain on his record-breaking 718-game AFL/VFL coaching career.
Speaking on the 'Dyl and Friends' podcast, hosted by former Blues teammate Dylan Buckley, Murphy said it was "definitely the wrong decision" for Carlton to get rid of Ratten, who is now in charge of St Kilda.
The 34-year-old said his relationship with Malthouse was strained from the time the former West Coast and Collingwood premiership coach arrived at Carlton.
"It was probably the most lonely I've ever been to be honest with you," Murphy said.
"There were times I just hated turning up to the footy club which is sad to say when you spend a lot of your life at a place where you should love, and I'd loved for quite a fair bit of my time there.
"There were times when I just hated turning up. It was extremely difficult."
Malthouse has since admitted Murphy was not his first choice as skipper, declaring Andrew Carazzo and Kade Simpson were higher in the pecking order.
However, Malthouse wasn't sure the pair would play in the team regularly enough to hold the captaincy.
"Initially when you get told you're captain, you like it to be a real positive sort of a period, so it wasn't a great start," Murphy said.
"There's no point in me coming out and bashing Mick Malthouse because he's one of the greatest coaches of all time.
"He's got the record for longest coaching so what am I going to do coming out and slamming him?
"But I just think his time at Carlton, I don't think he was really in it for the right reasons and once it all turned pear-shaped, it was all about him, unfortunately, at the end and I was left to be thrown under the bus quite a bit."
On the podcast, Murphy revealed he rejected interest from Richmond at the end of 2015 after the Blues had played out the season under caretaker coach John Barker.
Murphy played another six seasons at Carlton and reached the 300-game milestone in round 22 this year before retiring.
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