My experience: May be different for others...(pardon my terminology, I don't know all her move names yet)
Makoto's 3C is either going to come out or it's not, 2B, 5C deal with it, and 6C if you're fast to react (she can do similar things to your 5B that Noel can, so if she does get inside, get 2C out). You really have to think about what it is she's trying to do. Obviously the main goal is to get inside, where her punches are faster than Ragna's. But a good Makoto player can actually use her D punches to get inside safely. And unless they're really good at doing the Acorn Shadow Clone thing and mixing it up, 5D will deal with most of that. She may try Bandit Bringer or the 2-hit Chun-Li jump-in combo, if only to start her Space Counter Loop. She WILL use her DP if she thinks it's safe.
Space Counter Loop only works so many reps on Ragna, if they do too many and she gets caught in the air on a mistimed jump cancel, you get a free hit.
The hardest thing I tend to deal with are her mixups into her Pilebunker move. That's where Ragna has to learn how to fight at "max range" so that she can't get inside and mix you up. One of my means is 5D dash cancel 5B ID. Only dash cancel if you hit confirm the tip of 5D, also, using 6A for jump-ins, 5C for other aerial stuff.
Having a projectile means she can keep you from doing your usual pressure, so j.C is useful and Gauntlet Hades. Getting a counterhit on Gauntlet Hades (2nd part) is do-able, I think, but like I said, being familiar with max-range combos helps (combos that only use the tips of Ragna's hitboxes).
I have yet to see Makoto players actually use Space Counter for what it's for...even when they're cornered.