Few ways to go about it, really.
Up close you can pepper them with standing jabs - Sometimes I also SJab into Jumpin seeing as SJab Sweep isn’t as reliable considering Sweep has quite a bit hittable hitbox so SJab Sweep itself could get you crumpled at times. If they follow through with the FA you’ve hit them once already so the second hit (Jumpin) will knock them out of it into a combo - Failing that they can FDash or BDash - BDash can then be caught with a JFierce (Depending on how close you were when you jumped), FDash (Under you) may or may not be safe, or may or may not lead to you being punished, but not a lot of people would have to reaction to FDash and BDash is almost programmed as the safer bet in everyones head.
Don’t forget TAP - It has the same issue as Torpedo in that some FA’s can hit you before the TAP hits them, but as someone who uses TAP a hell of a lot, FA’s become less of a problem and instead neutral jumps and being stuffed happens far more than being crumpled. TAP can be used as a wakeup meaty for people who try wakeup FA’s when they see you at a distance and suspect a DS. In addition if you see someone charging an FA in your face, there’s tight timing but your TAP can completely ignore the FA hit - Been quite a few occasions where someone who was peppering their game with FA Dashes suddenly was close enough and ballsy enough to let rip with an L3 FA trying their luck. Neutral jumps, TAP or even a very delayed EX HB will knock them clean out of it, ignore it or just put you in a position to punish it.
In addition, as someone who uses CMP DS quite a lot as a blockstring and repeatedly to push people to the corner, depending on the character/hitbox, this’ll pretty much stuff all FA attempts other than ones done instantly (As in pressed and released immediately), which not many people do.
On the occasions I generate enough bar for SUPER, I always look for that LDS into SUPER on FA’s, or even a trusty plain old ULTRA.
Nothing gets people to stop repeatedly FA’ing than an Ultra or SUPER in the face, it makes you feel completely stupid for just handing someone all that free damage for nothing.
If someone is FA’ing close to you, the typical response is to FA right back - They either have to cancel it or risk trying for an L3. In most cases they release it and dash or dash cancel and allow you to dash, you get some Ultra bar and just need to watch your health (If they released it) otherwise you’re both back to square one.
I’m at a casual level where the above usually nets me free crumples because people are programmed and stupid enough to release their FA’s and FORWARD DASH into me as I’m charging an FA in response to theirs - God knows why they always do this but they do it anyway, eat a crumple and say hello to my favourite Back Dash TAP Ultra setup, thank you for the free damage you’re welcome don’t mention it.