If you don't want to stand still, you don't have to, and I rarely do either - making sure you're right where you want to be in relation to the ring edge, wall, and opponent is something you should definitely be doing while you're trying to bait your opponent. Standing still and whiffing for meter is something you do when they're being adamant about staying put, since it punishes them further for not accepting the disadvantageous situation that is running in.
If an opponent puts precedence on whiffing for meter over actually winning the round, then they either think they can surmount a comeback and win the round by rushing you and then comboing you (Cervantes, for example), which Raphael has good tools to prevent, or that they have you scouted and know that they can make up the damage in time for the round end.
I will admit that there are certain scenarios where it's probably not the best idea to let them burn meter - for example, the 10 seconds left in the round, you have full health and they have very little left, and they're trying to stock for the next round - but on a whole, just sitting and waiting with a health advantage means the balls is in your court to manipulate your opponent. Them building meter is generally not sufficient leverage to force you to rush in when there's a round at stake.
Raphael's guard damage game isn't really hampered by this strategy. To reiterate, it's not running away and just doing nothing but pokes for the entire match. It's backing off during times where even a correct guess put Raphael in an awkward or disadvantageous situation, and baiting the opponent to do something foolish so that you can punish with 236B, 6B(B), 3(B), or whatever tool you've used that works for the situation.
If you're constantly being the one that's forced to run in, however, you probably need to re-evaluate your game plan and playstyle.. These are things I have been doing and winning with - against players like Ramon and Partisan, mind you - and their rate of success tells me that they're most likely a vital part of their game.