Both areas are excellent destinations. How much total time do you have for this trip? What are your precise travel dates? September is a transitional month, weather-wise, but Seville could be extremely hot even at the end of the month. This year it hit 90 F or higher each of the last five days of September. You can check actual, day-by-day weather stats going back at least ten years on the website timeanddate.com.
There's precious little risk of really excessive heat in Santiago de Compostela, which is known for lack of sunshine even in mid-summer. Last September it managed to get up to 79 F twice, but some days stayed in the 60s.
Neither of these destinations will be particularly easy to reach from Portugal. Ground transportation links between the two countries are limited and infrequent. It is doable, but it may cost more time than you're expecting, and Portugal has a lot of worthwhile places besides Lisbon and Porto. Actually, if your trip is short, I wouldn't go to the Algarve--but I'm totally uninterested in beaches.