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IMO, this wasn't a message to Putin, this is a message to anyone in his inner circle who is plotting against him.
Similiar thing happened to Slobodan Milošević, former president of Yugoslavia and then Serbia. He was finally ousted in the 2001 Buldozer Revolution after evidence emerged that he murdered his political rival, Ivan Stambolić (also his former mentor). The successor government of Serbia couldn't properly try him because even though the evidence was solid that he was implicated, there wasn't enough evidence pointing out that he was the one behind it. - not to mention, Stambolić's death couldn't be confirmed because his remains weren't found until 2004.
Because Miloŝević could potentially walk free, the successor government shipped him to the ICC-Y in The Hague (there was a special tribune for former Yugoslavia), killing two birds with one stone - getting rid of Miloŝević and potentially preventing him from taking power while simultaneously restoring the relationship between Serbia and the EU as well as tactifully starting to repair the relations between the former Yugoslav states.
This is exactly the point of this arrest warrant - it's not like every country on Earth will uphold this rulling as many oppose the ICC themselves, nor the point is to restrict his movement outside Russia - the point is that it gives a bone to a potential uprising against Putin, whether done by a public uprisal (incredibly unlikely), or by inside forces and former/ostensibly current allies of Putin (much more likely), because whoever manages to upstage Putin and deliver him to The Hague in cuffs has potential leverage to become the next leader of Russia.
Finally, this is also to plant the more seeds of doubt into Putin's head - because everything that I said, Putin is most likely already thinking, which will further drive him paranoid - because anyone who has enough power behind the scenes has the potential to replace him and simultaneously get the approval from NATO and EU, as well as getting him behind bars in The Hague.
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