Stepping on the creature while walking is muttar even according to Rebbi Yehuda, since the Rabbanan deferred their issur in a situation of Mazikin. Why don’t we say the same according to Rebbi Shimon; that the issur miderabanan (of Melacha she’ina tzericha legufa) is muttar in cases of Mazikin, thereby allowing killing them on sight?
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Since Rashi mentions Rebbi Yehuda here it seems that the Shaala and the whole discussion is according to Rebbi Yehuda. If this is the case then the Gemara now learns that according to Rebbi Shimon you may indeed kill it outright.
Tosafos learns that the Sugya is according to Rebbi Shimon and disagrees with Rebbi Yehoshua Ben Levi. Perhaps Rashi agrees to this, that even according to Rebbi Shimon it should only be killed through Lefi Tumo. Other Rishonim learn that Lefi Tumo is not even a real Ein Mischaven, it is just a hidden way to kill it.
The reason to preferably kill it only in this fashion is that even according to Rebbi Shimon it is always better to avoid a Melacha as much as possible. Even if we can be Mattir a Derabanan for a Sakana why should we do so if there is the alternative of doing it in a way that, according to Rebbi Shimon, is completely Muttar? Ein Mischaven, according to Rebbi Shimon is Muttar Lichatchila in all areas of the Torah, even outside of Hilchos Shabbos.