This is a heady piece, Martineau's vocabulary is beyond enormous! I think, in short, he is saying that the moralist sees habit as the grand hope, we learn to build good habits but it makes religion less relational, which to the deeply religious is the despair of our faith.  

  "Nothing perhaps so clearly exhibits the true contrast between 'morality' and 'religion' as the different relations they sustain to the   'law of habit'.

Habit is the grand hope of good morals, but it is the despair of deep religion. 

If the moralist, in urging his system of right action, can but give us motive enough to begin with, his hardest point is gained; the great fly-wheel of the will once set in motion, the second revolution will be promoted by the first, so gain will build momentum, and the original impulse may suffer decline without much consequence.                        His maximum of force is needed only at the initial instant; and he is content, when the inertia of rest is overcome, to substitute the inertia of motion. 

But this, the last triumph of morals, is the total discomfiture of true  religion; which abhors the sleepy rhythm of a rotatory nature; which protests against changing the seat of duty from the center of soul, to the muscles of the body. 

The devoutest moments of each person's life are those in which they first create the rule which thenceforth they obey; and passes straight from the deep passion into high action; and bridges over the awful chasm between the world of sacred thought only, and divine vision. 

 True religion has no other office than to be ever pressing towards divine vision: it checks the spiritual encroachments of habit; compelling it to abide in the 'outer courts' and busy streets of action, and guarding from its invasion into the inner temple of the mind; to keep the eye intent  and the soul awake.