First things first, Ragna is not allowed to make mistakes in any of his match-ups, unless he wants to die.
Honestly, her mix-up is just as weak and easy to react to as Ragnas. Yes, she can parry your spacing, but only if you're being really predictable with it. 3C is beaten by 5C, like you said, yeah, but its slow and easy to see coming, so it's never been a problem for me.
Her DP gives her way better damage than ours gives us. But her DP's range is just as bad as her normals range compared to ours, so when you're spacing her, no, it shouldn't be a problem. Just bait it like you would bait Ragna or Jin or Tsubaki's DP. This match up is 5.5-4.5 for a reason, but it's also heavily dependent on Ragna controlling the space. If he can do it, it becomes near even.
Makoto uses meter at lot more than we think she would have to, it's just that she builds meter really fast that we don't notice that. If you're spacing and playing footsies correctly, there should be no problem with you saving your meter for damage.
Silly as this will sound, this match-up is only a problem if she's successfully getting in on you. Just keep her out, Ragna's built to do that, and you'll realize this S tier character is a lot easier to deal with than either CT or CS1.
For the record, I feel this match up is 5.2-4.8 in her favor. Shame match-up charts don't get that exact.