You didn't mention the rule set being used, but most specifically say that a batter running on the third strike, when not entitled to, is not a rule violation. The ASA rule is 8-7-P.
Also, to call interference you generally need a player interfere with a legitimate play. How did a throw to first to "retire" an already retired player interfere with a play against an active runner? There was no out to be had at first base, so there no play to be nothing to be interfered with at first base.
As an official you did your job (well, up until you called interference on a play where it shouldn't have been). You called the strike and called the batter out when she started to run. The rest is on the defense. It's an old line, but it bears repeating: The defense is responsible for knowing the situation and playing it accordingly. If they make unnecessary throws over and over again, that is something that their coaches should be addressing, not the umpire.
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