I don't think it has to be stigmatising, but I do think that calling things by their specific name helps with everyones mindset.
Some words like 'helpful' are fine, because it does wat it says it does. But calling disparate things by the same name leaves the door open for people to mentally align those things to 'be' the same thing, which they aren't. Distinction is important, even if the differentiation isn't black-and-white. Taking some aspirine vs. drinking a nice cup of green tea can both help with a slightly sore throat, but they are not the same thing. (at the same time, I'd argue that it's better to take that nice cup of tea, take a nap, eat healthy, get to bed on time etc instead of covering the symptom with aspirine)
Turning people away from a subject in itself isn't a bad thing; if someone is swayed that easily, they should probably not be entering a world of non-repeatable non-measurable non-transferable items and activities, especially if the people involved can't be held responsible for their actions. It also isn't a pharmacology thing on its own. While pharmaceuticals can help with certain issues, it's not the core of medicine and in certain cultures it's mostly just abused to cover up symptoms instead of used to mitigate or resolve root causes.
But it's a tricky comparison. In the end we're comparing something measurable with something based on feelings and traditions. Those are generally not that reconcilable.
Willow bark to aspirin is a great example of an extremely old “traditional” treatment becoming medicine. Same with quinine for malaria, etc. Tons of real medicines originated by isolating compounds found in nature, even if the final pill form you see is purified or even synthetic. Most people are unaware or just fine with this fact. Sure there are probably many natural treatments out there that are effective (and many that aren’t, or are downright dangerous). We should do the work needed to study them scientifically, and turn the good ones into medicine. Not just promote alternative treatments indiscriminately.
Keep in mind that there are traditional treatments that we haven't yet isolated the cause of action or the understand the pharmacology due to it being the interaction of different compounds.
I'm not supporting traditional or alternative medicine, but I also don't think that the issue is so black and white, and treating it as such turns people away from the subject entirely.