Or HaChaim on Numbers 31:6/אור החיים על במדבר ל״א:ו׳

1 וישלח אותם ואת פנחס, Moses sent them…together with Pinchas, etc. The reason the Torah wrote the word וישלח, "he sent them," was to make the soldiers participating in this campaign into שלוחי מצוה, delegates charged with the performance of a sacred duty, a מצוה. We have the rule that delegates on a מצוה-mission are safe from harm while performing their task. The verse repeats the word אתם to tell us that the presence of Pinchas with these twelve thousand pious soldiers doubled their effectiveness; Pinchas was equivalent in piety to all the other 12.000 soldiers combined.

2The fact that Moses selected Pinchas instead of Joshua to be the leader of this expedition was also an astute move by Moses. Pinchas had already demonstrated jealousy on behalf of G'd. Who could have served as better inspiration for the task at hand than Pinchas? He radiated more destructive power against negative spiritual forces than did Joshua. It is also possible that Moses was afraid of the people who would assail these soldiers wanting to know that if they considered themselves as so pious why had they not protested the involvement of their brethren in the harlotry and thus helped prevent such sins from being perpetrated? To head off such criticism Moses sent along Pinchas who had risked his life in order to bring this harlotry to a stop. Perhaps this is what the Torah alluded to with the unusual construction אתם ואת פנחס, "they together with Pinchas." Moses hoped that by his presence Pinchas would supply the missing factor, i.e. the preparedness for self sacrifice in order to stop others from sinning, something which even the pious soldiers had not contributed at the time of the debacle at Shittim. It is possible that G'd already originally intended that only someone of the calibre of Pinchas could wipe out the shameful stain which would remain on Israel's character if the Midianites were allowed "to get away" with what they had done. G'd was grateful to Moses' choice of Pinchas as the leader of this expedition. G'd Himself had not wanted to direct Moses to appoint Pinchas in charge of this expedition fearing that such a directive might have made Moses think that he himself was not qualified to lead this punitive campaign. The result of G'd's astuteness was that His desire was carried out without Moses becoming embarassed in the process.