Wouldn't it be easier to remove the great strength and toughness, and maybe do 15+2d6 or 20+2d6 for her str and Tough that a space marine has, and the augments, and just give them those to work with and have the player choose from the none astarties versions of the equipment? You know since Sister's of battle use very similar gear and such? I mean heck there is a Sister's equivelent for every one of the space marine classes except Libarian, and Machine Cultist.
For Battle Sisters and Inquisitors, I would not boost Strength and Toughness, but make available Astartes-grade armour and weapons - basically, giving them what the tabletop fluff says they have. The character would still be rather squishy (having about 3-4 points of resilience less) and not "pwn" as much in close combat, but at least be able to deal comparable ranged damage and thus feel like a valuable addition to the team.
For Battle Sisters, I would also recommend using the Inquisitor's Handbook version rather than Blood of Martyrs. A lot of people seem to think the latter is better, but I disagree - most of the miracles in there are "team boosts" that would only increase the badassness of the Marines even further, and for this the character pays with a more punishing advancement scheme where you'll need much more XP.
But I'll admit that I am also biased by the IH book's miracles being much more "toned down" and preserving the vague nature that the AoF have in the TT fluff, rather than giving them space magic that makes them cast forth rays of light from out of their eyes and other such things.
It should be noted that Sisters of Battle don't fit too well into the Deathwatch by nature of what they are. They are battle nuns/church police officers who work with the Ordo Hereticus. The Deathwatch, on the other hand, fight aliens. While there can be some crossover, it would be an incidental and sort of one time thing. And Inquisitor, on the other hand…
It is not so incidental as you may think. Battle Sisters may fight virtually anything and everyone, as an issue of White Dwarf once noted. Their list of battle narratives in the 3E Codex included several reasons for why they would attack any army in 40k, including all the aliens. If the GM really wants, it should not be difficult to craft a reason for their presence.
"Their fanatical devotion is a bulwark against corruption, heresy, and alien attack, and once battle has been joined they will stop at nothing until their enemies are utterly crushed. […] Wherever there are foes of the Emperor, the Sisters of Battle will be found fighting with faith and steel."
- 5E C:SoB
"Heretics take many forms. Most are lost humans, whose weak minds have been corrupted by the manifold temptations of a dark and sinister galaxy. None are immune - planetary governors, Imperial Guard commanders and even whole Space Marine Chapters have been declared heretic and been exterminated as such by the Sisters of Battle. Yet there is no stricture within the Ecclesiarchy that heresy is a purely human crime. Aliens can also be sanctioned as heretics - that the creed against which they transgress is not their own is of no account. Nevermore so is this true than of the alien who chances his army against the Emperor's Will by inciting rebellion, subverting the will of Imperial subjects or invading by force. Genesis matters naught - all heretics are damned, and all must be purged with fire, lest their apostasy gather a following."
- WD #382
This is more suited for a campaign of interconnected missions rather than some sort of official teamwork, though. Something like a single Sister Militant hanging around with a Deathwatch Kill-team rather than her own Sisters would be strange indeed. The easiest explanation would be to have her be a sole survivor that gets picked up by the Marines, and stays around to complete her mission and avenge her Sisters' deaths. There, problem solved.