Put the scare-quoted material in single quotes, just as you would do with any other nested quotation. It's not your responsibility to distinguish between genuine quotations and scare quotes in the source material--and if you put yourself in that position, there's a chance you could guess wrong, which could open you to charges of misquotation. (For that matter, you could be accused of misquotation for dropping quotation marks, regardless.)
Here is the quotation that I believe you were posting when the question of how to indicate the deletion of punctuation marks arose:
A mere voluntary courtesie will not have a consideration to uphold an assumpsit. But if that courtesie were moved by a suit or request of the party that gives the assumpsit, it will bind, for the promise, though it follows, yet it is not naked, but couples itself with the suit before, and the merits of the party procured by that suit, which is the difference.
And here is the quotation block after you decided to indicate your removal of the comma after the word before by adding a letter space and empty square brackets at the point where the comma formrly appeared:
A mere voluntary courtesie will not have a consideration to uphold an assumpsit. But if that courtesie were moved by a suit or request of the party that gives the assumpsit, it will bind, for the promise, though it follows, yet it is not naked, but couples itself with the suit before [] and the merits of the party procured by that suit, which is the difference.
Unfortunately, most readers will not recognize this method of marking a deleted punctuation for what it is intended to be.
When I was answering the question where the edited quotation appears (Archaic meaning of 'procure' - 1615 UK), I thought that perhaps you had intended to interpolate a word or phrase at the point where the brackets appear, but had forgotten to insert the additional word or words. Obviously this isn't a desirable result.
Especially in legal texts, exact replication of the original wording is extremely important, and any omission—even if, as here, it is of nothing more than a comma—should be reflected in the altered version of the text with ellipsis points. But replacing
couples itself with the suit before, and the merits of the party procured by that suit
with
couples itself with the suit before...and the merits of the party procured by that suit
is overkill, since, as you note in the body of the question, it invites readers to imagine that one or more whole words have been removed from the quotation.
The most sensible way to deal with situations like this one is to bite the bullet and keep the original punctuation—even though you feel that it makes the sentence vastly more confusing. As it happens, a tendency toward comma overload (by modern standards) is common in seventeenth- and eighteenth-century English (and American) writing. In the long run, though, you'll be much better served by adjusting your notions of appropriate comma use to accommodate (and make sense of) the older style than by punching holes in quotations by removing punctuation marks whose omission you must then signify in one or another unsatisfactory way.
In this example, I'm not at all sure that the sentence would have been more coherent if the author had omitted the comma in the first place. But regardless of how you come out on that question, I think that resisting the urge to delete punctuation marks in legal quotations is a very wise policy.
Best Answer
The classical punctuation to denote emphasis is the exclamation mark.
However, that applies to the whole sentence. It is sometimes possible to draw a word to the end of a sentence to emphasize it instead of the whole sentence:
Or if the word in question is an interjection, put it between dashes:
Another alternative I have sometimes seen is putting the exclamation mark into parentheses behind the word.
But in general, emphasis of single words is achieved via formatting, not punctuation.
Historically, this has been italics, or, since, italics are hard to emulate in handwriting, underlining in handwritten documents. With the advent of typewriters, the underlining convention was reused but on computer terminals, underlining no longer works because you cannot shift the carriage position back in a text document (which is how underlining was achieved on typewriters).
This is probably when people began to hint at emphasis by prefixing and affixing a word with underscores:
_like this_.In newsgroups, many people switched to slashes,
/like this/. I have no idea where the asterisks come from though.