The Saints had been courting Aleer for well over a year, but during the trade period they stunned by pulling out of the deal.
The GWS defender ended up re-signing with the Giants for two years.
St Kilda have been busy in the last few days, signing Carlton free agents Tom De Koning and Jack Silvagni and then securing trades for Gold Coast midfielder Sam Flanders and West Coast forward Liam Ryan.
They also farewelled captain Jack Steele to Melbourne and retained ruck-forward Rowan Marshall despite his wish for a trade to Geelong.
But their backflip on Aleer raised eyebrows and Lyon said he was pleased the Giants backman still had an AFL home.
"'Renege' is a strong term, I'm not sure that's exactly correct," Lyon said when asked about Aleer.
"Nothing's perfect. A deal needed to be done and they certainly weren't throwing him out the door or pushing him out.
"I'm really thrilled that they saw him as we did - a high-calibre player, extended him for two years.
"The human side is always difficult, but it's worked out really well for him. In simple terms, I'm really pleased for that.
"Life's messy, football's messy, trade period is messy."
Lyon declined to go into the reasons around why they eventually decided against trading for Aleer.
"There are always the 'known knowns', right? But there's a lot of information," he said.
"Every trade period you go through, you're trying to figure out stuff.
"There's a lot that goes on within the trades and decisions or non-decisions and non-trades.
"It's not as simple as what's on the surface. There's a lot of threads to get a trade executed."
Overall, Lyon is rapt with St Kilda's recruiting drive. In August, they also re-signed young gun Nasiah Wanganeen-Milera on a massive two-year deal.
"It's a remarkable achievement for a Melbourne club that hasn't had success for a little while, so kudos to our list management team," he said of recruiting De Koning and Silvagni.
"And then obviously we also recruited Sam Flanders and Liam Ryan, so four 'bona fides'."
Lyon praised Steele as a "really strong leader" and said they were adamant about not letting Marshall go.
"We really value him," Lyon said.
"We think we come out of it, on the whole, in a positive. But as the president (Andrew Bassat) said, we're in the fight - we're all really looking for improvement."
Lyon was emphatic they can make the De Koning-Marshall ruck combination work.
"Clearly we have a strategy. I have some pretty smart coaches around me. Corey Enright is top of the pops with football IQ," he said of his assistant.
"Hawthorn went to three flags playing two ruckmen. The game lends itself to talls, you look at Brisbane - Darcy Fort, Oscar McInerney...
"Their ability to compete in the air, in the ruck was pretty pivotal, wasn't it?Â
"We'll have to work through that."
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