Sometimes, I mix up the english (or in my case german) keywords of different kanjis, when the meaning of the keywords is very similar. To avoid this with words which I regularly mix up, I write in braces behind the keyword that it's not the other one.

Do you think this will hurt my learning process?

I did that in some cases and managed just fine, for other cases I would write down both the kanji (or sometimes three) that I thought it might be and passed it if one was right.

I've started replacing my english keywords with japanese vocab now, so I don't let this slide any more for the cards with japanese keywords. They have to be 100% right.

No. That sounds helpful. I did the same thing.

In those cases I usually add the ON reading of the character, so that I can quickly spot the correct one among several alternatives. Not only that, but also helps me reinforce the ON reading of the character at the same time, and greatly reduces the number of failed kanji caused by mixing of synonyms.

I recommend this approach because when you need to recall a kanji (when you have to write a letter, or from a word you just heard) your first clue is usually its ON/KUN reading, and once your mind visualizes the phonetic part of the kanji (that you study in RTK2), the rest of the kanji comes naturally from context.

Another advantage of this approach is that in words composed by two kanji with the same meaning, like 宇宙 or 完璧, having memorized the phonetic component means that you'll always write these words in the correct order.

However, there are some cases in which this trick doesn't work, for example 散 and 撒. In those cases, I use KUN reading.

Nope, it's not cheating and in fact is pretty smart. The decks I have include Onyomi and Kunyomi, sample words in kana, other English meanings. I also do as you did adding the Kanji that it's not if there's similar keyword meanings.

You might find yourself doing similar things when you move on to vocabulary. Don't hesitate using it there either.

I always add either a German or a Japanese vocab item there, to differentiate it.
It's not cheating, it's making the whole process easier by removing the confusion that naturally arises when Heisig used strange English words for the Kanji.

And according to Heisig himself, simplifying the whole learning experience is what it's all about.