Just found this article, really nice to read.
http://thoughtality.com/the-spitfire-wing
It looks like the decision was really influenced by the need to accommodate 8 guns.
A trapezoid wing with rounded wingtips comes close to the "ideal" elliptical wing.
And as Kurfurst mentioned, the advantages of truly elliptical wing are more theoretical than practical. Just in 1934 when the wing was designed it all looked a bit different than during WWII. Average performance of fighter planes was much lower and they probably saw the need for good low speed handling and efficiency. As performance and speed increased these aspects were less important. Also the 8 guns in wings design became obsolete with introduction of more powerful canons.
Back to the original question. I believe the 109 performs worse than the spit at very low speeds, because when it has to deploy slats, the wing is already working far behind its optimum. The spit can achieve similar lift without slats and with lower angle of attack. So yes, the induced drag would be lower. (I don't want to dig into boundary layer separation and stall questions)
At the same time Kurfurst is right, that this aspect became obsolete during WWII.