Option 1: The Easy Way
It's called the easy way because you just ditch Faith Points completely! That's right. Let's look at another codex that gives each squad a specific power they have to test for to use: Codex: Grey Knights. They don't roll for the number of times they can attempt to use their Psyker powers, they just test.
To compare with the Test of Faith, the Psyker test is dangerous due to Perils, but is generally a little more reliable. The Test of Faith rules from the White Dwarf codex are not dangerous, but are far less reliable unless under certain circumstances. At best, they both have a 1-in-6 chance of failure. The Test of Faith requires 3 things to achieve this level of certainty: 1) Squad has suffered casualties, 2) the lead Character (Superior or Mistress) is still alive, and 3) a "faithful" Independent Character is with them. If you've just deployed them from your table edge with no Independent Character, they're at whopping 50% chance to succeed their test. I personally think that's enough of a penalty without additional limiting factors.
This does change a few things, however. The biggest one is the standard Troops Battle Sisters Squad. Their Act of Faith is very flexible. I think the best way to handle it is to just say that a specific unit can only use their Act of Faith once per turn. In turn, some should be reworded to something like ". . . until the beginning of your next movement phase" instead of the end of the turn. Most are fine since they're for your specific shooting or assault phase. Here's the version of Grace of the Emperor from my Ophanim Bike Squad in this option: You can choose to apply either Skilled Rider or Hit & Run to the unit until the beginning of your next movement phase.
Option 2: The Slow Dicey Way
This time we'll keep the Faith Points, but we'll make it scale. Instead of reverting to the old static points per game method, we'll make it a bit more random but still keep it based on the units you take. Each unit will roll a d6 to determine if they grant a Faith Point. The target number is based on the unit itself. A unit that still has its Superior alive gets a +1 to this roll (so if the unit is listed as needing a 5+, they'd only need a 4+).
- Saint Celestine: Always grants a Faith Point. If she joins a unit, it also automatically grants a Faith Point.
- Canoness and other "faithful" HQs: Always grants a Faith Point. If joining a unit, that unit gets a +1 bonus that stacks with the Superior bonus.
- Celestians (also the Sororitas Command Squad): 3+
- Sisters Repentia: 5+
- Battle Sisters: 6+
- Dominions: 5+
- Seraphim: 4+
- Ophanim: 5+
- Retributors: 5+
Option 3: A Faster Dicey Way
Let's just give each of the above listed units a d6 and give a Faith Point for each 4+. Easy day. HQs can still give a Faith Point without a roll. I'm not a monster.
For both options 2 and 3, you'd only roll for units currently on the table. Any points not spent by the beginning of your next Movement phase are lost and you roll for more.