Spouse Visa Issue

[Terpe]

.... As I understand it, she would have to go through entry clearance again and this time on a marriage visa. My concern is, will she be considered as having an immigration history if she does this, as we did not go through with the marriage in the UK?

Hi there MK, welcome here.

You are correct, if she returns and you marry in Phils she will need to apply for spouse visa and comply with all requirements.

Each visa application is reviewed on it's own merits. There will be difficulty in your circumstances provide she does not remain in UK after expiry of her visa.
Just provide short explanation in your support letter as sponsor.