This is very strange. The Perseus text of Josephus (linked by LSJ) follows the Niese text and shows ὑποκατέβησαν τοῦ μὴ εἰς πλέον ἐναντιοῦσθαι ("they relaxed from not opposing them"). In Niese's original text & commentary (ca. 1890), the apparatus criticus for this line shows only one variant reading (ὑπεκατέβησαν) in only one MS. No trace of any form of ὑποκατακλίνω. The dictionary's ὑποκατεκλίσαντο (you're probably right about medio-passive rather than active) may be someone's emendation, but it's hard to say whose, because the Niese text seems still to be the only text of Josephus available. More likely, that "ὑ." in LSJ may simply be a mistake: sometimes it happens with those Oxford people (I've seen them make a mess of Empedocles, for example).