Space Marines are a rapid strike force and not the official military arm of an enormous (and hugely wealthy) organization.
You're still forgetting the Frateris Militia and the Clergy itself. The Sisters of Battle are a symbol and the core of the Church's military might, but they are not the Ecclesiarchy's "rank and file foot soldiers", as you make it sound. Those would be the faithful. All of them.
There are quite a lot of major Ecclesiarchy facilities lacking any sort of SoB protection, such as the Subsector Cathedral on Bladen, which was said in Codex Cityfight to be defended solely by its attending priests and a regiment of Cadian Shock Troops.
"Imperial Shrines form the main defence points against an alien invasion. If a Chaos, Ork, or Eldar army descends upon a planet, the citizens would usually rally around the Frateris Clergy and defend their shrines and temples from the alien invaders."
- WD #212
"Preachers are sometimes known as Defenders of the Faith as they and their Militia often form the first line of defence against insidious Chaos and Genestealer cults or other heretical sects. When a planet is subjected to an alien invasion, it is the Preachers who mobilise the population into defending their homes from the godless heathens who attack them."
- 2E C:SoB
Why would the Ecclesiarchy have such a tiny force? They're highly trained people in power armor. There's nothing artificially keeping their numbers down as in the case with the Space Marine implant process or rules limiting size of Chapters.
Except extremely high requirements in terms of physical and mental attributes, the likely massive cost of equipment (further exacerbated by simmering distrust with the Adeptus Mechanicus), and maybe a certain degree of scepticism from those who think the Ecclesiarchy is already skirting the borders of the Decree Passive. Let's keep in mind that, initially, the Church Militant was supposed to not have any standing armies at all , and that the Battle Sisters are essentially a condoned oversight.
Going by the 2E Codex, it took the Ecclesiarchy 2.500 years to create the six Major Orders that exist now (with Ecclesiarch Deacis VI having founded the Orders of the Sacred Rose and of the Bloody Rose in late M38), which I assume took considerable political scheming and much preparation over several generations of the clergy so as to lobby for general acceptance of a military build-up from an organisation which had earlier plunged the Imperium into civil war. The Convocation of Nephilim, which ultimately bound the Sisters of Battle as allies to the Ordo Hereticus, is a direct product of this fear.
And after M38, only the Minor Orders were founded, which gradually took over local matters so as to free up the "Big Six" for waging the larger campaigns and act as the Ecclesiarchy's rapid response force, active throughout Imperial space and beyond (as we can see on the Force Disposition Charts I linked).
Oh, and did I mention that the Sororitas have so few members that they can afford to have their novices take their vows on Holy Terra itself, in presence of the Ecclesiarch, in a ceremony with no more than 500 novices attending?
Also, you can ask the same questions about Space Marines, actually. The only reasons as to why there's not more of them is because there is the Codex Astartes deliberately limiting their combat capabilities (kind of like the Decree Passive, mhm?) and because they are intentionally limiting their own recruitment capabilities by requiring potential recruits to exhibit such useful battlefield skills like "blacksmithing" (Salamanders), and because their only source of recruits is the fiefs they have been granted to govern by the Administratum, much like the Sororitas recruit solely out of the Schola Progenium. Why is the Imperium not founding many more Chapters?
So you see, there are a lot of similarities between these two forces, even beyond their equipment and combat prowess.
I'm sorry for having dragged the thread off-topic a bit, but I can't just leave some of those posts uncommented, lest I would allow GW's original fluff to be muddled further by lack of public awareness. As you may have guessed, this is a subject I feel somewhat strongly about, and whilst I have no problem with people intentionally dismissing GW's own fluff in favour of something else, I won't stand idly by when it is communicated in a manner I perceive as flawed and thus misleading for others who might prefer the original background.
Feel free to use Codex fluff to back up your statements, however, like I did. Not just personal preferences/opinion.
Edited by Lynata