Praise be to Allah, the Lord of the Worlds; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.
Here are the answers to your questions.
1)If I buy a packet of halal instant noodles from an online shop who receives my payment with a non Islamic Payment gateway, does it make my purchase haram?
The fact that the non-Islamic payment gateway is involved in forbidden dealings – such as benefiting from the amounts deposited and transferred through it in usurious dealings – does make it forbidden for you. Dealing with someone who deals with riba (interest and/or usury) in what is permissible is something permissible.It is forbidden to help others in sin, because Allah, may He be exalted, says (interpretation of the meaning):
“Help you one another in Al‑Birr and At‑Taqwa (virtue, righteousness and piety); but do not help one another in sin and transgression. And fear Allah. Verily, Allah is Severe in punishment”
And the Prophet (blessings and peace of Allah be upon him) said:
“Whoever calls people to guidance will have a reward like that of those who follow him, without that detracting from their reward in the slightest, and whoever calls people to misguidance will have a burden of sin like that of those who follow him, without that detracting from their burden of sin in the slightest.”
Narrated by Muslim in his Saheeh (4831)
And there are other texts which prove that the one who helps someone else in sin is also sinning, such as the text which curses the one who records riba and the two who witness it, and the curse on the one who carries alcohol (to someone who will drink it) and on the one who presses (the grapes etc with which it is made), and so on.
But not every kind of help is prohibited; rather what is prohibited is deliberate help in which the one who offers it intends to help the person in his sin, or direct help such as carrying alcohol or writing down contracts involving riba.
With regard to indirect help, when one does not deliberately intend to help in sin, this is not prohibited; if it were to be prohibited, it would cause a great deal of hardship to people.
The issue of helping in sin and transgression was the subject of a lengthy discussion and debate amongst Fuqaha globally. To sum up it is generally agreed that helping in sin and transgression falls into four categories:
1. Direct and intentional help, such as someone who gives alcohol to another person with the intention of helping him to drink it.
2. Unintentional, such as selling prohibited things that have a permissible use, if there is no intention to help them in using them in prohibited ways.
3. Intentional but indirect, such as someone who gives another person money with which to buy alcohol. That may also include indirect manslaughter.
4. Indirect and unintentional, such as someone who sells things that may be used for lawful or unlawful purposes, and does not intend to help those who use them for unlawful purposes, such as someone who gives another person money not for the purpose of buying alcohol. If he buys alcohol with it and drinks it, there is no sin on the one who gave him the money, so long as he did not intend to help him with something unlawful.
This fourth category also includes buying and selling and renting from the mushrikeen and Muslims who are evildoers, and giving money to them in charity. In essence the first three types are clearly haraam while the fourth type is permissible, when it is not direct or intentional.
Thus, the permissibility of dealing with non-Islamic payment gateway that is involved with prohibited dealings when buying instant noodles depends greatly on the intention of the party using it or it is a direct action in helping sins and transgressions.
When you know that there is a syariah compliant payment gateway that is not in anyway whatsoever involved in prohibited dealing but still uses a non-Islamic payment gateway that is involved in prohibited dealings, it would mean you are intentionally and directly helping in sin and transgression that is clearly prohibited and haraam.
2)Does conventional payment gateway earns RIBA from transactions would it make my halal money haram?
Money is fungible. It is neither haraam or halal. Money is just a medium of exchange to facilitate transactions. However, the transactions can be haraam or halal. In the lifetime of a single unit of currency (eg. RM1) it could have been used in a haraam transactions (buying alcohol, gambling, etc) before being used to buy halal food in a halal restaurants. Money will keep going in and out of haraam or halal transactions. So your money is neither halal or haraam. Nonetheless, when you use your money to directly or intentionally help others in this case a non-Islamic or conventional payment gateway to commit sins and transgression, your action is prohibited and haraam. You should use a syariah compliant payment gateway where you could avoid such sins and transgressions.
3. Would this mean that the manufacturer of halal goods who earns the proceeds of sale from me has incurred RIBA through the conventional payment gateway and this money is has mixed with stolen money, money from interest and money acquired through other impermissible means, will the halal goods buy from the online Store be halal or haram?
Like you the merchants or manufacturer are required to avoid helping others from sins and transgressions. The income they earned from the sale of goods to you may be permissible but the payment transactions that they received from you via a non-Islamic payment gateway that is involved in forbidden dealings makes them party to sins and transgressions that are prohibited and haraam.