Radwraith said:
Let the ship's Arch Militant lead a Squad (Or larger group) tasked with stopping a SM incursion. While the assault marines use your armsmen to grease their chainswords the the Squad Sergeant (A lvl 2 or 3 DW marine) rolls in on the PC. Unless the AM is VERY powerful 2-3 rounds later the Marines are headed for their objective!
This assumes you fight the marines in conventional warfare. Why aren't people considering things like tenebro mazes to funnel attackers, murder servitors/crew reclamation combinations to go all Borg on their asses, Alien mercenaries, EM weaponry that will jam their power armour, stealth and cloak systems to avoid detection… there are any number of ways to beat marines that aren't as straight forwards and suicidal as "fight them on their own terms".