Hello sir, if your wisdom tooth is creating pain and discomfort, it's better to extract it, because it's an extra, non-functional tooth, which may create ulcer in your mucosa due to constant irritation... So, it's safe that you extract it...
For bad smell, after extraction, do a general cleaning and polishing followed by chlorhexidine mouthwash and brush twice daily...
Health Tips
Do warm saline gargle...