It’s totally OK to do whatever you want! The health cost to magic helps a lot. As GM I also had intelligent foes often prioritise the magic users because… well you would focus on the person who can make fire come out of their fingers.
As others said, I’d “balance” them with eventually giving the martial classes amazing feats/techniques/physical ability. But the key thing I would do is make them general, things they will use often and for different reasons, rather than specific (like magic). I feel like that’s the main difference between magic and martial.
Eg.
FREE-RUNNER: Move over basic terrain obstacles without roll (if you can narrate how), more difficult obstacles (eg. high wall) are EASY rolls
CAT-LIKE REFLEXES: always first to move, re-roll failed reflex saves, HARD to hit (if aware of attack), etc
NINJA: Move silently, climbing always Easy, Dex rolls EASY, surprise attacks always hit and do MAX damage
BAR-FIGHTER: Use any object as weapon - bigger objects = more dmg dice + can hit more targets, breaking stuff is EASY
KUNG-FU: When attacked by multiple foes, if they miss redirect their attacks to each other (use your dmg dice). Single foe is EASY to hit and HARD to be hit by. Re-roll failed mental saves.
BEZERKER: Each time you take damage in an encounter, increase damage dice by 1 and reduce damage taken by 1. If offended or frustrated, intimidation is EASY.
INDOMINANT: When you would drop to 1hp, roll CON to stay on 1hp. If on 0HP, self-revive on 19 or 20 roll.
BEAST-BOND: If in the right position, your pet adds damage to your hits, can take hits instead of you, makes relative perceptions rolls EASY.
You could also simplify it by just using a TAG or 1 liner (eg. Big Bar Brawler) and whenever the player does an action that the TAG reflects they are good at (eg. throw the table at them, challenge someone to drinking game, punch him in the face, intimidate, etc), simply give them advantage (re-roll failed attempt). This really encourages players to creatively play their character like they imagine, and gives the martial classes a totally unique and more flexible mechanic to the magic ones.
Of course the simplest solution is just cool items 
Main piece of advice: Don’t worry about this until you need to. Whether its a cool new item or technique, you can give your martial classes these things when the magic classes begin to feel much stronger in your campaign.
The joys of being a gamer in a 3rd world country… I’ve been writing and putting things on DTRPG just to make enough to reinvest in the community by picking up books like these lol