I vote for Grand Company seals. At the current moment Grand Company seals are a hassle to earn once all GC quests/missions are complete and seems like a very fair exchange for something that people worked towards earning only to have taken away later and considering other options such as Gil which may be something these people would not have worked towards earning (either already being rich and not needing Gil or preferring non trade-able items such as the items you would purchase via Guild Marks).
So in my personal opinion it's better to exchange Guild Marks for GC seals however there is one issue which is the Grand Company seal cap of 30,000 (the current cap for the highest rank of a Grand Company as far as patch 1.20). Not sure how many Guild Marks most people have but I know a quite a few people (including myself) has well over 30,000 with myself having 60,000 alone just for THM.
While I would prefer to trade every Guild Mark I have at once for GC seals at a 1:1 ratio and basically forfeit everything past 30,000 (as opposed to obtaining Gil) I think it would be best to allow the player to pick which class and how many marks they want to trade (in the same form you would sell items). This way a player can trade in up to 30,000 Guild Marks (obtaining 30,000 GC seals), spend the GC seals, and have room left for more to trade in more Guild Marks for more GC seals so nothing goes to waste.
As this is my personal opinion, I'm sure others oppose this idea and would prefer Gil to GC seals seeing as how many people are not interested in items obtained through GC seals and would prefer Gil since currency can buy anything and everything trade-able. Well, in a perfect world where everyone gets their way (excluding people who think the hard work of others should go unrewarded simply because it gives them an advantage over those being lazy and/or not being present at the time to do such work) then SE would allow an exchange NPC to appear (perhaps until 2.0 is launched) where players can choose between GC seals, Gil (hopefully at a much higher ratio than 1:1), or something else SE deems worthy of being exchangeable for (such as Ifrit Totems or Moogle Nuts at a 1:1,000 ratio?).
The above proposition may be to much work for the programmers of the game to bother with for a game undergoing such drastic changes that this may too too much time (I'm not too sure about this stuff, I'm not a programmer) but it would seem like having 2 NPCs would make this much easier. 1 NPC would allow the player to pick the Guild Marks of which class they are trading in for a universal token (for example you would trade 1,000 Gladiator Guild Marks for 1,000 Guild Tokens) that way programmers wouldn't have to write code to allow players to select an item from their inventory and choosing the amount then thrown into picking which item they want to exchange for and picking that amount. Then the 2nd NPC would have the items available for trade using the universal Guild Tokens.
Edit: Or the programmers can just turn all Guild Marks into Guild Tokens instead if there is no reason to distinguish which class the Guild Marks belong to which would be even easier.