It seems that the milk in a calf of an Eglah Arufah is forbidden because the rule is (see MISHNAH BECHOROS 5b) that anything which comes out of something Tamei is itself Tamei . Since it is forbidden to derive benefit from an Eglah Arufah (see MISHNAH KIDUSHIN 56b and Gemara there 57a that since "atonement" is stated in connection with Eglah Arufah, it therefore is forbidden to derive benefit from it, as is the Din for Kodshim also - see Rashi 57a DH KE'KODSHIM) it would follow that the milk of the Eglah Arufah is also forbidden for Hana'ah.

However, milk actually found in the Keivah (stomach) may have a different Din. See CHULIN end 116b that milk found in the Keivah itself is Pirsha be'Alma and does not have a Din of forbidden food. See SHULCHAN ARUCH YD 81:6 and PISCHEI TESHUVAH there #14 that according to this, even the Keivah of an impure animal is permitted.

KOL TUV

D. Bloom