I am not an authority on the subject, but since nobody replied to you in 3 weeks, I will take a stab on this.
> but we are hopeless that she could be expelled
First off, nobody will expel your new wife, because you will not want to be in a situation where she will be in Romania past her 90 day visa, unless you have managed to either extend her visitor visa or immigration allows her to get a 1 year permis de sedere based on the fact that she is your wife and you guys want to be together while the paperwork is been processed for family reunification.
>Â ... a policeman from emigrants from my hometown gave me some hope telling me that if Im married with her, it's ok no one's asking for health
Please do not make this mistake of listening to this type of advise, it is non-sense. Everybody must have a clear immigration status at all times, while in a foreign country, the fact that you are married with someone gives one the right to apply for family reunification, but not to overstay a visitor visa and technically be illegal in the country. It could cause you much headache down the road.
> but it was just a piece of advice from his experience but officially everyone talks that they have to come back and apply again
And how would she come back to apply again? By requesting a new visitor visa from the Romanian Embassy in Manila? That makes no sense either.
First you need to understand what would be the 'normal' process, regardless of what you like or dislike.
The process is:
1. She visits Romania
2. You guys get married
3. You submit all paperwork to immigration for family reunification
4. If approved she gets contacted by Romanian Embassy in Manila regarding medical tests and/or other paperwork she might need to submit.
5. Finally she would get the permanent immigrant visa from Romanian Embassy in Manila.
Now, is it possible that after you get married you can go to immigration in Romania and ask for a visitor visa extension (passed the 90 days) or a 1 year temp permis de sedere because you guys want to live together during the approval process? Sure. Whether or not you she can get that, I have no idea, however you would need to do it as soon as possible, right after you get married, such that there is enough time to allow for the application to be processed and she would not be in Romania with an expired visa.
If everything works out and she can get a visa extension, she might need to go to Manila to do medical tests and pick up her papers, I am not sure whether she can do this part of the process from Romania, you will find out.
All I want to say is 1). Make sure she is legal in Romania at all times and 2). Take a day off from work, go to the closest immigration office in the morning, take a ticket, tell the immigration officer your story and what you would like to do and ask for advise/opinion. Specifically as it relates to the possibility of a visa extension or a temporary permis de sedere, while waiting for the family reunification process to move along. Do not ask them about anything related to Manila Embassy, they won't know, for that part you can send them an email asking what is relevant to that part of the process. It's only going to cost you 1 day. Then you will be better informed.Â
Good luck to both of you.